After just about 3-4 weeks of zero problems, last night I had my first real, "oh no this is bad" feeling. Let me say that this may not be a 'Vista' issue... I think it could have happened with XP.
I had noticed that when I had added files to my desktop, that I could not delete them. I would get an error message stating that the file or folder was corrupted and not readable. Oh man that's a bad feeling. I noticed if I did a "shift delete" bypassing the recycle bin, I could delete file. Some quick googling produced a know issue with a corrupt recycle bin. It was a simple fix, delete the system recycle bin folder, and have the system automatically recreate it.
That didn't fix my issue.
The next thing I found was to run a disk check from the disk tools section of the "Manage my computer" section. Checking the boxes to automatically fix errors while scanning the disk. Since this was on my C:\ drive, I would get a message when initiating a scan that it could not do it on the active Windows partition, and kindly asked me if I would like to schedule to do this at startup, awesome.
Except, it never did it at startup.
I was starting to get stressed. Would I need to do a clean install? Crap, I didn't want to do that. Repair? I decided to boot from the setup DVD and see if something caught my eye. I clicked the 'repair my system' option and was presented with a ton of options, there it is... command prompt!
At the command prompt, I dropped over to the C:\ and ran C:\chkdsk /f, it asked if I wanted to dismount the primary drive, uhhhh scary, but yeah, I guess so. Then it fixed all the corrupt files, found no bad sectors, and once I rebooted back into Vista 64, all seems well.
So now why did my files get corrupted? I don't appear to have any data loss either.
Moral of the story? Sometimes there is a quick fix, it just takes time to get to it. I wanted to wipe the system, and start fresh, but couldn't bring myself to something that drastic whithout exhausting all my options.