I suffered this problem very seldom, about 10 times since I got my N900 in Feb 1, 2010.
I used always the standard kernel with all official fixes.
The last time it happened I used the KP50 kernel.

I say from careful observation:

1. it is not a software (app) problem, though it may be triggered by some kind of usecase with 3G data and GPS at the same time.
"top" shows no process going wild, when the fast energy loss is in progress. This is not a Maemo/app process problem!

2. on the N900 there are much more (embedded) processor cores than just the main ARM CPU. My guess is, some of those cores which serve the 3G/UMTS radio (phone) or GPS or audio codecs or whatever crash, or run endless loops, which will not show up in the Maemo-Linux process tools.
Or even some hardware has an internal, temporary shortage. Yes this is possible, but it all this is impossible to track down on a living N900, and one would need very expensive test equipment to analyze it. No luck.

3. If you note that battery indicators (I use Battery Eye) drop fast, reboot the phone immediately, after reboot the problem will be gone - until the next time...