On windows the files are never deleted. The mod is not used because it was overwritten, but it's never deleted.

This still seems to cause duplicate mod problems even though the mod is just a text file with "D" in it, FML still considers it a mod.
Windows has an issue with deleteOnExit(), something to do with having any reference to the file being active stopping it from working.

Running as an admin should fix it for the most part. Since in the Win world its considered a High level command to allow a program to delete things on exit. Create a patch hook that forces a run admin silent. Your not sending out a virus so it shouldn't be an issue. Make sure you place a disclaimer however or you can get in trouble with people.

7 and higher this a greater issue. You may need multiple permissions nodes.

Worked around in #31

Um I have not had this issue. ... are you sure it is an issue?

Check the folder. If you remove a mod from the server, then on windows the file will not be deleted. However, the client will not use that mod anymore which is possibly why it seems like it's not an issue.

Aw that makes sense.