Did you use the standoffs built into the case or did you add them yourself? Can you show us a picture of the rear I/O? Usually if the standoffs aren't there or something like that the rear I/O ports won't line up well with the cutout.
There were built in standoffs and I just used them, and I put the I/O of the motherboard inside the case, and fitted it nice and neet. But now I see, the I/O has a plushy thing stuck on it, is this normal? Is this done so that motherboard cant touch metal of I/O??