leetnoob: congrats at finding the problem. I've never noticed my Debian apt-get pegging the cpu like that, but I've always run it from the command line, never from Synaptic. And it does tend to bog down the phone, but I usually just let it run and I go off and do other stuff.

I've only very recently started experimenting with overclocking my N900, and only when I want to do video recording or Gimp photo editing. Then I boost the CPU's frequency, but, more importantly, I switch from "on demand" to "user space", which seems to be the N900 equivalent of the N8x0's "performance mode".

EDIT: (you probably have, but) Have you tried using fsck both on the MyDocs partition and on the image file?