Maybe your battery indicator is acting up. Apple recommends draining the battery once a month to keep the indicator accurate.
Maybe try restarting. Elsewise, hope it's a glitch, because users who've had battery probs sometimes seem to have a hard time shaking them despite firmware upgrades. Apple said iOS 5.0.1 was supposed to fix battery bugs. Then it also said iOS 5.1 was supposed to fix them. But I read that battery bugs can be hard to fix, because there are so many variables in user settings, involving push, location services, etc.
5.1 has taken my battery usage from 8-10 hours or heavy use downtown about 2-3 hours. Also,it now take almost 6-8 hours to charge the device. VERY disappointed.
I wouldn't let it go fully dead. 5% or so is good enough to calibrate the meter. I don't think batteries like being fully dead. Just a thought.
It's only an issue if you leave them exhausted for a period of time. A day or two is fine. Even when the iPad shuts itself down the battery is not fully flat.