Actually, it may yet be a problem on this end. My ancient binary based on 0.93 doesn't do it, but current does. And my WIP NEStopia port (also using SDL) doesn't do it either. I'll bet something isn't getting shut down properly.
Incidentally, on FC5 or other modern distros you can usually restore the right mode by blind-typing 'xrandr -o 0' (that's lowercase O then the number zero). If your focus lands on an xterm/konsole/whatever after MAME exits, that'll usually work, although sometimes I don't get mouse control back.
UPDATE: That wascally Giles no longer calls osd_quit() from the core, so SDL_Quit() is therefore missing too. Yeearrrgh.
ONCE MORE WITH FEELING: Fixes are now up on my blog - both a "test1b" full archive (which in reality only changes src/sdl/sdlmain.c) and a zip with just the changed file.