Some additional information might be helpful
What version of CHDK are you using? If you are using something older than 1.4, it might be worth trying the current version. If you do try a different build, keeping a backup of the build and cfg files you are currently using is a good idea.
What scripts are you using? If you are using one you wrote or modified yourself, please attach it.
CHDK shouldn't spontaneously change settings itself, but some scripts might change the autostart setting. Of course, if you set it to "once" it should be cleared after the cameras reboots once.
a further annoyance on the ixus 70 is that it seems to sometimes default in to taking raw files too.
The most common cause of this is accidentally hitting the raw shortcut key in alt mode. You could modify your script to disable raw at startup using the set_raw function.
You can also set the autostart value from script using
http://chdk.wikia.com/wiki/Script_commands#get_autostart_.26_set_autostart but if it's really changing by itself there must be some other problem.
I think that the normal menu settings are stored in a config file on the card - is there any way to get them right then make this file read only?
The settings are stored in the CFG files. It is possible to set the normal FAT "read only" flag on files, but I don't know offhand whether it actually stops the firmware from writing the files, or what impact it would have on CHDK.