Well, first off, Advanced Power tends to take a little long to initiate in my experience.

Also, in my experience, the yellow (it's actually technically orange - yellow looks a bit different, and in my experience is always a sign of an error - but you'll know it when you see it. If your device is still working, and shutting down/not-booting, you're probably getting the orange light - but it's similar enough to yellow when you have nothing to compare it to), anyway, that light never blinks when charging when the screen is on. I am pretty sure it only flashes when screen is off (I think the logic is, when it's on, you can see the battery icon).

So overall, I'm not sure how much of your problem is your N900 being broken right now. It doesn't seem too bad.

*Sigh* I really don't know what's going on with Advanced Power wiping out everyone's Battery icons from the status menu.

Did you install from Devel, Testing, or Extras?