BTW it may be completely unrelated, but I had issues with key mappings in the past - and found that I when I saved a new config file, some of the mapped keys were appearing as very large integers:
e.g.
keyOptions = 1073742048
I think it may have been the OSX build, probably around 1.7-1.8. I put it down to a bug in that release and just c&p'd these large keycodes around in the config until I got access to the functions I needed. Using the 'normal' keycodes in that build resulted in unresponsive keys.
There's a narrow possibility it was an earlier Windows build though - I have a Win VM on my mac for portable Atari dev..... (yes too many machines & platforms - ugh)
D