Is there a trick to access the ALT behaviour of the buttons under chdkptp?
As you have noticed, when chdkptp runs, button clicks work as if <ALT> mode is not enabled so that you can control the camera remotely.
To expand on this slightly:
chdkptp works by sending lua script to the camera. The buttons in the gui just send a click("key name") call. Scripted key presses in CHDK (whether from PTP or a script you run from the menu) always go to the stock firmware, not CHDK keyboard handling code. It would be useful to be able to send key presses to chdk (so you could navigate the alt menu remote, for example) but we don't currently have this capability.
You need to issue a command to chdkptp to have it run a script. I have that sequence written down somewhere but I'm not home right now. Probably reyalp will comment at some point here - if he hasn't I'll post later when I did up my "cheat sheet".
To run a script on the camera, you generally want to use something like this in the chdkptp console
lua loadfile('myfile.lua')()
loadfile loads the file and returns a function. The following () executes the returned function. The reason to use this instead of the more obvious dofile() or require() is that code executed in these functions cannot yield, which means you can't use sleep or keyboard functions.
Note that while the script is running you will not be able to control the camera from chdkptp using the key buttons or any other script commands. If you want to have a script that runs for a long time on the camera, but still be able to control it over ptp, you will probably need to write your own script using the ptp message interface. Some examples of this in the chdkptp lua code lua/rlibs.lua msg_shell and lua/multicam.lua