I did some searching and stumbled accross this post on the Microsoft Answers Forum:
Copying images from Compact Flash Card Reader on Windows 7 x64 corrupts some image files.
This morning I got up and paid the $9.99 for the Fast Picture Viewer Codec. So I installed it like they said, I rebooted...etc. Wow, now I can see my .cr2 files in the explorer window. But the question is did it fix the problem I have been battling for the last 5 months?
Yesterday I imported 313 photo's from a shoot, and was getting the smeared, corrupt, partial processed in both LR3 and different or same ones in Bridge CS5.
After installing the above program, I made a new test folder, imported the same way I always do with LR3. I have checked LR3 and Bridge CS5 and I cannot find one corrupt looking file. I am not getting to excited yet, but this seems to have fixed the problem. I am so far very very happy to say the least. My next big shoot is on Sept. 25 (wedding) I will let everyone know what happens on import of those files. Oh, I also opened up my recycle bin and recovered a couple of the corrupt looking files from yesterday and now they look fine. So this may be the fix. Maybe I am over excited but rendering seems to be quicker on my large 5D MkII raw files.
Have a great day.
Sean