Q:

SQL Server 2012 Express fails at repair install, produces error 5178

My SQL Server Express Service will not start up.
To produce this problem, I basically cloned my old hard drive (Which had SQL Server Express 2012 installed) to a new hard drive (Seagate Momentus XT 750).
EDIT: I am adding info on how I cloned my hard drive as per request of SQLRockStar.  I used Seagate DiscWizard.  The program was producing errors when trying to clone the HD when using the simple "clone HD" command.  So I "cloned" it the following way with the help of SeaGate Tech support:

Place new Hard drive(Momentus XT) in slave slot, Old HD in Master)
Create backup image of old HD and save on Old HD.
Create Seagate DiscWizard Bootable CD
Physically Swap both hard drive positions, (old now is in slave, new is in Master)
Boot with Seagate DiscWizard Bootable CD and restore backup image of old HD onto new HD.

Afterwards, I tried starting SQL Server Express 2012 on my Momentus XT and it would not start.  So, I tried performing a repair installation of SQL Server, and it failed: see summary below:
Overall summary:
  Final result:                  Failed: see details below
  Exit code (Decimal):           -2061893608
  Start time:                    2013-08-12 15:53:13
  End time:                      2013-08-12 16:13:13
  Requested action:              Repair

Setup completed with required actions for features.
Troubleshooting information for those features:
  Next step for SQLEngine:       Use the following information to resolve the error, and then try the setup process again.
  Next step for Replication:     Use the following information to resolve the error, and then try the setup process again.

Machine Properties:
  Machine name:                  MATT-LAPTOP
  Machine processor count:       8
  OS version:                    Windows 7
  OS service pack:               Service Pack 1
  OS region:                     United States
  OS language:                   English (United States)
  OS architecture:               x64
  Process architecture:          64 Bit
  OS clustered:                  No

Product features discovered:
  Product              Instance             Instance ID                    Feature                                  Language             Edition              Version         Clustered 
  SQL Server 2008                                                          Management Tools - Basic                 1033                 Express Edition      10.0.1600.22    No        
  SQL Server 2012      SQLEXPRESS           MSSQL11.SQLEXPRESS             Database Engine Services                 1033                 Express Edition      11.0.2316.0     No        
  SQL Server 2012      SQLEXPRESS           MSSQL11.SQLEXPRESS             SQL Server Replication                   1033                 Express Edition      11.0.2316.0     No        
  SQL Server 2012                                                          Management Tools - Basic                 1033                 Express Edition      11.0.2316.0     No        
  SQL Server 2012                                                          LocalDB                                  1033                 Express Edition      11.0.2318.0     No        

Package properties:
  Description:                   Microsoft SQL Server 2012 
  ProductName:                   SQL Server 2012
  Type:                          RTM
  Version:                       11
  SPLevel:                       0
  Installation location:         c:\215ca8b216eb992f2f4a\x64\setup\
  Installation edition:          Express

User Input Settings:
  ACTION:                        Repair
  AGTDOMAINGROUP:                <empty>
  AGTSVCACCOUNT:                 NT AUTHORITY\NETWORK SERVICE
  AGTSVCPASSWORD:                <empty>
  AGTSVCSTARTUPTYPE:             Disabled
  ASCONFIGDIR:                   Config
  ASSVCACCOUNT:                  <empty>
  ASSVCPASSWORD:                 <empty>
  CLTSTARTUPTYPE:                0
  CLTSVCACCOUNT:                 <empty>
  CLTSVCPASSWORD:                <empty>
  CONFIGURATIONFILE:             
  CTLRSTARTUPTYPE:               0
  CTLRSVCACCOUNT:                <empty>
  CTLRSVCPASSWORD:               <empty>
  ENU:                           true
  FAILOVERCLUSTERGROUP:          <empty>
  FAILOVERCLUSTERNETWORKNAME:    <empty>
  FTSVCACCOUNT:                  <empty>
  FTSVCPASSWORD:                 <empty>
  HELP:                          false
  INDICATEPROGRESS:              false
  INSTANCENAME:                  SQLEXPRESS
  ISSVCACCOUNT:                  NT AUTHORITY\Network Service
  ISSVCPASSWORD:                 <empty>
  ISSVCSTARTUPTYPE:              Automatic
  QUIET:                         false
  QUIETSIMPLE:                   false
  SQLSVCACCOUNT:                 NT Service\MSSQL$SQLEXPRESS
  SQLSVCPASSWORD:                <empty>
  UIMODE:                        AutoAdvance
  X86:                           false

  Configuration file:            C:\Program Files\Microsoft SQL Server\110\Setup Bootstrap\Log\20130812_155231\ConfigurationFile.ini

Detailed results:
  Feature:                       Management Tools - Basic
  Status:                        Passed

  Feature:                       Database Engine Services
  Status:                        Failed: see logs for details
  Reason for failure:            An error occurred during the setup process of the feature.
  Next Step:                     Use the following information to resolve the error, and then try the setup process again.
  Component name:                SQL Server Database Engine Services Instance Features
  Component error code:          0x851A0018
  Error description:             Could not find the Database Engine startup handle.
  Error help link:               http://go.microsoft.com/fwlink?LinkId=20476&ProdName=Microsoft+SQL+Server&EvtSrc=setup.rll&EvtID=50000&ProdVer=11.0.2316.0&EvtType=0xD15B4EB2%400x4BDAF9BA%401306%4024&EvtType=0xD15B4EB2%400x4BDAF9BA%401306%4024

  Feature:                       SQL Server Replication
  Status:                        Failed: see logs for details
  Reason for failure:            An error occurred for a dependency of the feature causing the setup process for the feature to fail.
  Next Step:                     Use the following information to resolve the error, and then try the setup process again.
  Component name:                SQL Server Database Engine Services Instance Features
  Component error code:          0x851A0018
  Error description:             Could not find the Database Engine startup handle.
  Error help link:               http://go.microsoft.com/fwlink?LinkId=20476&ProdName=Microsoft+SQL+Server&EvtSrc=setup.rll&EvtID=50000&ProdVer=11.0.2316.0&EvtType=0xD15B4EB2%400x4BDAF9BA%401306%4024&EvtType=0xD15B4EB2%400x4BDAF9BA%401306%4024

  Feature:                       SQL Browser
  Status:                        Passed

  Feature:                       SQL Writer
  Status:                        Passed

  Feature:                       LocalDB
  Status:                        Passed

  Feature:                       SQL Client Connectivity
  Status:                        Passed

  Feature:                       SQL Client Connectivity SDK
  Status:                        Passed

  Feature:                       Setup Support Files
  Status:                        Passed

Rules with failures:

Global rules:

There are no scenario-specific rules.

Rules report file:               C:\Program Files\Microsoft SQL Server\110\Setup Bootstrap\Log\20130812_155231\SystemConfigurationCheck_Report.htm

The following warnings were encountered while configuring settings on your SQL Server.  These resources / settings were missing or invalid so default values were used in recreating the missing resources.  Please review to make sure they don’t require further customization for your applications:

Service SID support has been enabled on the service.
Service SID support has been enabled on the service.

The following resources could not be configured during repair without additional user input.  Review the warnings to understand your next steps:

The service failed to start for an unknown reason. For more information, see the event logs and the SQL Server error logs.

I looked at the error log and it said

Error: 5178, Severity: 16, State: 1
Cannot use file 'c:\Program Files\Microsoft SQL Server\MSSQL10.SQLEXPRESS\MSSQL\DATA\master.mdf'
because it was originally formatted with sector size 4096 and is now
on a volume with sector size 3072. Move the file to a volume with a
sector size that is the same as or smaller than the original sector
size.

I read that last error message and am really confused.  I'm led to believe that this is a problem with SQL Server, My HD has 4096 sector size.
UPDATE:
More information:  I have discovered that My old hard Drive was 512 physical sector size and my new HD is 4096 sector size.  I hear that there are conversion issues between the two sector sizes, but SQL Server is the only program that is producing errors on my system, I don't understand it.
UPDATE:
I have attempted to uninstall SQL Server and reinstall it.  It did not succeed in installing the instance.
UPDATE 9-6-2013:
I have "Fixed" the problem by installing SQL server on a fresh install of windows 7 on the hard drive.  Then I tried cleaning up some things by moving the new partition to the beginning of the hard drive and erasing the problem partition.  Then, I couldn't boot into windows with that drive, then, the drive wasn't seen by my bios.  so... I returned it!
I guess this is just one of those anomalies...

A:

The Momentus XT is an "Advanced Format Drive" and I see that you are running Windows 7 SP1.  If the drive runs 512e mode this can cause you a problem with SQL Server.  This is because it can create sectors in some multiple of 512 byte boundaries, instead of always at 4096 bytes. (Your error was caused by a 6 * 512 byte sector.)
If that is the case, then you will need to take some corrective action. Microsoft has a blog post and a KB article for Windows 7 and Windows 2009 R2 on this issue which points on to other links.
http://blogs.technet.com/b/filecab/archive/2011/04/26/using-4k-sector-and-advanced-format-drives-in-windows-hotfix-and-support-info-for-windows-server-2008-r2-and-windows-7.aspx 
http://support.microsoft.com/kb/982018 
If this is your problem you may want to download the latest FSUTIL to investigate. http://www.microsoft.com/en-us/download/details.aspx?id=8903 
This has not been the fix for everybody. In the MSDN forums I found a lengthy set of responses with various fixes.
http://social.msdn.microsoft.com/Forums/sqlserver/en-US/5c090e72-e83d-4fca-a087-75a3df5d2b4f/localdb-cannot-start-strange-error-in-log-contains-sector-size-4096-and-is-now-on-a-volume-with
From this discussion you will see that some finally resolved their problems by updating drivers.

