I'm very sure that "fully recharging before flashing" is not the problem at all as I normally reflash two or three times per week and haven't seen such problems *related* to it.

Hard to say. Check which processes are running and how much CPU they take (e.g. by installing load-applet or using "top" in the X Terminal)?
What 3rd party software is installed? Only Extras catalogue, or also Extras-Testing or Extras-Devel?

Does going to "Offline" mode for your IM accounts improve battery life?