Also, in the CHDK menu (not the alt one)
The "menu" you get with a 3 second delay after entering ALT mode is a "help screen". It's meant to provide hints for new users (some people find it annoying and turn it off right away). It can be switched off from the CHDK menu: CHDK settings -> Menu settings -> Show <ALT> help screen.
Arg. So that actual delay is indeed on purpose. Damn, OK. Now I understand the logic of that alt thing...
Now this seems to somehow match the key masks. Also, in the CHDK menu (not the alt one), the buttons seems to work very well, so what makes you think this is the problem?
Now I think that there is not problem 
Well, still, in the help menu, the buttons are not catched properly. But looking at the code, it seems related to the definition of SHORTCUT defines. It's a bit annoying that this help is documenting not handled buttons...
Alright well, I guess the main remaining problem now is the zebra/bottom glitch area.