Ok, so I know whats wrong, and how to fix it (well fake it anyway) but not why.

I got stuck on version 6.4, like everyone else that got stuck. After googling around, I found one post that mentioned having a double modules directory (modules, and modules/modules)

Turns out I have that. So when I update, I need to copy it all into modules/modules as well - because somewhere in the bowles of my database there is one or two references to modules/modules/fubar... So, note to self, remember to copy updates TWICE.

I guess when I move to drupal 7 I can fix this for good.

(Hey, and now, finally, drupal knows the time! Whoohoo!)