I just checked in an assembly and I noticed that the parts are showing up under the assembly (as I would expect) and also in the project folder. Neither instance of the parts are links and they have the same file names. Any idea what might be causing this?
Yeah, I have no idea why it would do that. I guess it doesn't hurt anything, but if you care about fixing it you could try deleting the assembly from the vault and checking it in again. But you would lose any old revisions if there are any. Or maybe try moving one of those parts to a different project and then movie it back and see if that changes anything.