Here's an interesting one,
I've created a batch script in maya (python) that grabs the contents of a directory and for each file found (.3ds in this case) it imports the file, changes the rotation to the one used by maya, freezes the transformations and deletes the history, quadrangulates everything if it is triangulated and then saves it out to a maya file.

All goes fine and it does its job, its just that once completed all the .3ds files in the original folder are locked and cant be deleted without shutting down maya and restarting it. I'm on Windows XP if that helps.

I've had a look into file referencing and if for some reason this is affecting it but I dont think it is.

Cheers
Simon