I too haven't figured out when Windows Explorer saves the column settings and for which folders these settings apply.
If some unmodified files appear as modified, the most likely reason is that you use different CVS clients. For example WinCVS uses a different date format than stanard CVS from https://www.cvshome.org/. If you check-out the repository on the command line and from then only use CVS Shell Extension or the command line, then there should be no problems. At least that's true for NTFS. If you have a FAT file system, you may need to run an "cvs update" when daylight saving time starts and ends.
The overlay icons don't work on Windows 95 and 98. I have tested only Windows 2000 and XP, but on Windows 2003 and Windows ME they /shoud/ work.
I'm using the command-line cvs.exe from cvsnt v2.0.41a for my checkouts. In my experimentation, I deleted one of the files showing up as modified, removed it from CVS\Entries, and used 'cvs up <file>' to check it back out. It immediately showed up as modified in Explorer.
I'm using NTFS on XP Pro, so now I'm really curious about the overlay icons.
If I get some free time, I'll check out the CVS package at cvshome.org and see if I get a different result.
Regardless, this stuff is pretty trivial - I wish I would have found this a long time ago. :) Thanks for the quick response.
Looks like the timestamps written to Entries are off by an hour when I use the CVSNT cvs.exe; if I switch to the latest from cvshome.org, I get a different timestamp, and CVSExt reports the files correctly.