The Thunderbolt has an issue with staying in sync with the battery. If you were to make a call or something the system takes a few minutes to catch up. So if you got off a call and put it right on the charger, your not allowing the system to catch up, thus causing the system to stop charging when it thinks its 100% when it really isn't. Then next time you take it off it will try to make up for what you did last that used battery, causing the 100% to 80% or whatever it may be.
To make sure you get a full charge on your device you need to reboot it and then place it on the charger. This allows the system to stop the charging when it really needs to be shut off. I always restart my phone before charging just so i know i get 100% charge.