I have the exact same problem, both with the unclickable files and the duplicate folders in windows explorer.
I installed a patch, which resets windows explorer in attempts to fix the problem; however, it did not work.
Here's the link to the kb tha I thought would do it:
An update is available that improves the performance and reliability of Windows Vista
If anyone has experienced this and found the solution, I would be most appreciative if you would provide some insight.
Thanks!
jdincinci