MBP Delayed (not slow) boot up?

I have had my MacBook Pro for over 2 years now (mid 2007ish). It is the version last sold before the unibody version came out (if only I had waited a bit longer!). It has recently developed an issue where after reaching a critical battery level (anywhere from 9-15%), the laptop merely turns off. It appears, from the status light, that it has entered sleep mode half the time, the other half I get nothing from the light at all. To a certain extent, I would expect this from a laptop with no energy, but when I plug the laptop back up to a constant power source, I get nothing from it for a good 10-15 minutes. It sits with the charging light lit, in an idle state. It responds to nothing, pressing the power button, removing the battery, resetting the PMU... so far I've tried everything I know to do. After that period of time, it spontaneously wakes up at random times with no stimulus it seems. Luckily I have apple care and took it in for repairs, they replaced the Logic board, which seemed to fix the issue for one day and then it reverted to its faulty functioning. Do I need to keep on going back to Applecare? I'm a college student with a need for my laptop, and they estimated 4 days last time, which turned into 2 weeks! Any suggestions on fixes?

Oh and one or two more details, I have little hdd space left on my machine (2 gigs). I'm not sure where all my space went to but Its hard to clear it all out while still keeping all I need. Maybe this has somethign to do with it? Seems odd for that to relate to a seemingly random start up delay. Also, if it dies with a charge of 10%, then sits charging for 10 minutes, it still will wake with only 10%, so it appears it has a will of its own!Thanks for your help ahead of time!

1) Back up all your data (if you haven't done so already)
2) Try an Archive and Install to avoid having to reinstall applications.
3) Still have problems after that, do an Erase and Install and start from scratch. If the new logic board didn't fix it, something's corrupted in the OS.

Another note: I think you need to at least 5 gigabytes of space to run Leopard properly and allow it some breathing room. Take off at least 10 gigs or invest in an external hard drive. The computer has to account for alot of things on startup - having a full hard drive seriously increases your startup times.

GrandPerspective this app will help you determine what to move off. Make room!