This has come up in a document library, and I can't find anything
about it on the web.

The library has mandatory check-out and Major versions enabled. A user
uploaded a Word document and checked it in, then checked it back out,
made changes, checked it back in. On check-in, Version 1 disappeared,
and versions 2 and 3 were created. Both versions are identical,
however if I use Compare documents on them, Word lists the changes,
but both versions look identical (In this case all of the changes were
comments, and they showed up in both Version 2 and Version 3, but Word
claimed they weren't in Version 2.)

I was able to replicate this once, but not a second time.

There appears to be another document where this has happened several
times.

After this happened, I removed the "Delete Versions" from the User
Permissions in Central Admin, so if it happens again, I know that it
wasn't a user deleting the old version.

Any suggestions?