I have a similar issue. I swapped out my battery with the additional one in the Costco bundle. I had charged it using the spare battery charger. All day yesterday it said 100% but when I got up this morning my phone was acting oddly and battery still said 100%. I tried to power off and it hung, so I did a battery pull. Upon restarting, my battery was at 5%. I'm recharging now and when I get to 100%, I'm using Root Explorer to delete the /data/system/batterystats.bin and restart. Not sure what else to do.