Windows booted fine, and I think all my normal services started fine. It was just one 3rd party service that had a fit. Searching for the full error in Google turns up people hitting this on older Windows versions, with Windows specific services also being impacted by whatever weirdness is going on. I guess Microsoft fixed all of their instances where it could break things, but not every 3rd party. Seeing references to a lot of different apps breaking due to this.

Here is the exact dialog that pops up.
Originally Posted By: File Name Warning
There is a file or folder on your computer called "C:\Program" which could cause certain applications to not function correctly. Renaming it to "C:\Program1" would solve this problem. Would you like to rename it now?

It also has a checkbox with an option "Don't perform this check at startup" along with buttons to rename the file or ignore it.

I think Peter's explanation is probably true. Some old API likely allowed paths with spaces, and didn't quote the path. Makes me wonder if there was something similar for the older "Documents and Settings" folder.

I should probably stop wondering why MS stuff works like it does, before I suffer some sort of elder god style madness.