Your problem may be related to init run levels and the scripts that are supposed to be run during boot/shutdown. There is a script for copying hardware clock to system clock at startup and shutdown. There is also a script for detecting if you are booting the device for the first time (starts 'startup wizard/clock set thingy).

Perhaps as you are 'hijacking' the boot sequence only half of these scripts are occurring. Maybe the system boots, does not copy hwclock to system clock (leaving system clock full of garbage), shuts down and copys garbage system clock to hwclock.

The n900 was never designed to be started this way, the startup scripts are less than bulletproof (they make a lot of assumptions i.e. NO ONE WILL EVER INTERRUPT PREINIT right? RIGHT??).