Yes I engaged with co-pilot, they believe it is something with R2 managing SC code below 6.5x. R1 is working great for us though :) So I am going to stay parked there for awhile. 
I just upgraded from Enterprise Manager 6.4.3.8 to 2014 R2. I have to move from Java 1.6x to 1.7 Update 45. I also went from Sql express to 2008R2 Mssql. The upgrade went fine, but now all my Storage Centers disconnect every couple of minutes then re-connect. The EM logs  show this for each: 7/10/14 4:46:28 PMWarningStorage Center xxxx xxxx is down [SN: xxxx]!Setting Primary to FailedStorageCenter Anyone else having issues with 2014R2?  One thing I will try tommorow is re-generating the Certificate on the Storage Centers. Reason being is after I upgraded my workstation from 1.6 U45 to 1.7 U45 to accomodate the new EM client, I could no longer connect to several of my Compellents via  browser. I could only connect to one. I realized after several hours that the SSL cert for the one I could connect to had the certificate created with the DNS name. The others I could not, the certs were generated with the IP address. Creating new cert through Storage Center using the DNS name fixed that, and they re-connected in EM again as well. Yet they keep dropping every couple of minutes. I am now wondering, and will try this tommorow, is I only re-generated the certs with the management ip dns name. Looking at the wizard again, it seems to want dns and ips of the controllers as well. Maybe this new EM is failing due to that. Anyway, just curious others experience with R2? Thank you! 
Anyone deployed Enterprise Manager 2014 R2 yet?