In the past, there were inconsistencies between the the Win32 and the DOS version as far as recording/playback goes. However, I sent a note to the developers pointing out the trouble. They kindly fixed the problem, and as of MAME32 b34b2, I no longer believe there are compatability problems between the two.(posted 9926 days ago)I record all of my games using the Win32 version and have had no troubles verifying them with the DOS version or verifying at least three dozen other input files downloaded from this site. I've also verified half a dozen of my Win32 recordings using the UNIX version at work. (Gasp! MAME at work?? Don't tell!)
My experiences show that it is probably much more important to have the same version of MAME regardless of platform and that specifying a platform during submission may not be necessary.
If you're a Win32 user, get the lastest beta! ;-)
-Thunky