Okay so first, Nover 3 is not compatible with the CX II (yet), so do not expect it to work at all. I only know this because I caught some nspire devs talking about it somewhere and might be misremembering but given that it's not working for you it's probably correct. It's also not too much of a priority because all nspire games until now were written to run at the CX I's 180 MHz and the CX II runs at over double that. You should definitely not need to overclock to run e.g. gpsp.
Even on newer CX I models (like my rev AB), the auto overclock doesn't work (it actually got stuck in a boot loop that required a filesystem reformat to fix). In any case what I ended up doing was to just save the highest stable overclock values and restore them manually on a reboot (these settings were 204 MHz, 204 MHz, and 68 MHz). Then just disable hibernation (regular sleep doesn't use that much battery power anyway) and you will basically never have to worry about it unless your battery runs out.
Actually, something else that is to be noted is that the default AHB frequency was waaay to high (94 MHz, with >66 MHz being considered dangerous according to Nover 3's readme). So overclocking-related things have definitely been changing before they even started working on the CX II. It is a wonder it even ran on my rev AB (in ndless's compatibility mode).
