I do not know
I ended up switching to XP in the end to resolve the issue and then found that RetroArch kind of sucked on XP end ended up using Mame directly as you described
I think my thoughts for using RA initially where to utilise the different cores. If I had to start trying to get different emulators running different things then I may have hit some problems and kinda thought that I would have made things easy by using RA in this way... the Pi manages quite well so guess that had some influence too.
As it happens light guns and Linux don't mix very well (or at least Mame gets confused) so switched it all out for XP, had I not, your comment would have had me probably kicking myself a little and I would have pursued that angle so thanks. Hope this at least helps other confused wanderers like myself out there.