In pre-intel powerbooks there was an additional battery for the ram which allowed you to switch batteries without losing ram contents. After the switch to intel this battery was no longer available.
Most likely is that there was a difference between the intel and ppc architecture on how it managed interrupts (can be used to wake a computer). I would disable bluetooth wake and wake on LAN and see if there is any difference.
Interesting. This sounds like a good explicans for my explicandum. Thanks for the input!