Photomerge CS5 not as smooth as CS3?

I am having problems with Photomerge in CS5 EX. I am creating a pano with 9 jpg images using auto align. When PS has merged the images I can see all of the transitions. Hard lines almost no blending. I took the same photos and opened them in CS3 and they blended nicely. Almost no work needed to be done other than crop.
Back to CS5>automate>photomerge>blend images together >OK
Bad results again. This time parts of image are not even aligned. Boat cut in half etc. Too much work even for the spot healing brush. Content aware only works in very small areas.
Thank you for your help
Adobe Photoshop Version: 12.0 (12.0x20100407 [20100407.r.1103 2010/04/07:14:00:00 cutoff; r branch]) x32
Operating System: Windows Vista 32-bit
Version: 6.0 Service Pack 2
System architecture: Intel CPU Family:6, Model:15, Stepping:7 with MMX, SSE Integer, SSE FP, SSE2, SSE3
Physical processor count: 4
Processor speed: 2400 MHz
Built-in memory: 3070 MB
Free memory: 591 MB
Memory available to Photoshop: 1632 MB
Memory used by Photoshop: 71 %
Image tile size: 128K
Image cache levels: 4
OpenGL Drawing: Enabled.
Intel Core 2 Quad Q6600
3 GB RAM

Could be that part of CS5 is now sitting on a bad cluster on your hard drive.
Your Video Card or CPU fan is spinning slow or has dust bunnies blocking cool air.
Go into Vista's Event Viewer. A hard crash will be listed in there. Gather the information and post it here. Maybe one of us can figure it out.
Go to this website and use this MS fix it. It is free and fixes a lot of issues with XP and Vista.
http://fixitcenter.support.microsoft.com/Portal

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