Each Mame update has a variety of new roms and sometimes changed Roms. These are Roms that are redumped to fix earlier errors.
You will have problems with a rom set from mame .56 and mame36 final. Not with all roms, but with some that have been changed up to that point. I think, though, that usually they will simply fail to load
The problems you report are strange though. It sounds likely that you have some other problem on your system. ArcadeOS should show no speed difference regardless of what mame, roms, or anything else you are using. It is a completely independent piece of software.