upgrade to win2k8 will not fix mis-alignment nor any of the block copy tools (SRDF/Timefinder/Open Replication/Open Migration/PowerPath Migration Enabler).  You really have one option, build new LUN, properly align it (if you are still on win2k3) and then migrate data to it either via backup tool restore or host based copy (robocopy).
If win 2003 is upgraded to win 2008, will it fix alingment offset issue with SAN disks?   I need to migrate storage from DMX4 to VMAX and existing LUNs have alignment issue, so customer said that they might upgrade it first to Win 2008, do think it will fix alignment issue?   Also if I use Open Migrator, which is block for block copy, I think it will not fix it, am I right? 
Alignment Offset