I did a bit of experimentation before leaving for work and removed the entire file directory, ran mamewah and exited immediately, stuffed the values by hand in the config file again and it ran fine, so this is definitely related to the files directory, you don't have to do a full re-install after all,just wipe the files directory.
When I ran it the 2nd time it gave me an error 70 "access denied" and quit. By the way the error occurs after I select a game to launch, while it's loading the game, I don't know if it helps in anyway (would mame and mamewah try to access a file at the same time?)
I started over methodically documenting what I was doing, saving the files directory after each run, but as luck would have it, it ran just fine the 2nd and 3rd time. I'm guessing it's just a matter of time until it crashes again, and when (if) it does I should have a full copy of the files directory to compare it to.
I'll keep you posted