Thing is, the actual shutdown stuff is based on voltage. If you ever look at battery-eye's voltage logs, you will see the voltage all over the place during normal usage. The "percentage" is just a rough estimate, barely more than a guess based on current use and voltage.

This also means that if you use your n900 heavily until it shuts off, the voltage will have been pushed lower than "normal" by the heavy usage; letting it sit before powering it on will give ot a chance to recover a bit and go back over the poweroff threshold.

To use a different metaphor, it's like a car battery: crank the engine until it stops turning over, wait for 10 minutes and you'll be able to get some more cranking out of it.
Run it dead with a smaller load - like leaving your headlights on - and you probably won't.