ive had a experience just like this Last Monda, my problem was a little diferent in some ways. I have a stock 6.5 rom, and i was wanting some sort of program for battery usage. Cause I always have extended batteries i use Seidio 3500 mah batteries i have 2, when 1 goes dead i swap it out with the other i use a solo battery charger to charge the spare 1.
i ussually get about a days worth of use out of 1 of these 3500 mah batts.
I searched around and found this thread
http://rolandsdottir.blogspot.com/2009/10/windows-mobile-battery-life-tips.html
about half way down it suggests a couple battery programs to use if you have battery problems i did the global switch to cdma only and installed the Dot freds task manager and Dr sig stat battery watcher. both programs seemed awesome but i noticed within a few hours that my battery that was at 80% was down to 10%. i did a hard reset and then it was all back to normal again, not sure if these programs or thread will help you guys out or not.
is there anything i should do with the tp2 to have it recognize the different size batteries, everyonce in a while i will have to use a wall charger and when it is at 100% it will still take about 2 hours for the indicator light to turn green for the full charge.