If you have an identical version of MAME and MAME32, they will support the exact same ROMs. MAME32 uses the core MAME base, and adds a GUI to it. All changes are done at a GUI level, not at game driver level.
If you use two different versions (even only a couple of revisions apart), then some ROMs will not work in one when they work in another.
ROMs change all the time. As game drivers get fixed, corruptions in dumps are discovered (and sometimes the oher way around too). What you need to do is use a ROM auditor to make sure the ROMs you've got are the right one for MAME.
ClrMAMEPro is probably the best ROM auditor around.
Website:
http://www.clrmame.com/EasyEmu guide on how to use it:
http://www.mameworld.net/easyemu/clrmameguide.htmClrMAMEPro can merge two sets of ROMs to make sure only good ROMs get upgraded, and can in some instances even fix problems with bad ROMs. If you're doing a big upgrade between MAME versions, you should always run all of your ROMs through ClrMAMEPro and verify their correctness.