As I said in another thread, I experienced this problem with 1.6 frequently. Sometimes it would charge to full, other times it would be at 88% - 90% when I picked it up off the charger. I "solved" it by charging my phone from my work PC, for whatever messed up reason it doesn't happen if I charge it from a PC (my home computer is set to sleep so I never hook it up to that one as it would never charge, but my work PC doesn't sleep so I leave the cord at my office).
After a bit of surfing on the issue, I've come to realize that it is not an uncommon complaint. I've just been letting it roll off my back though, since I am never short on opportunities to charge the thing during the day. So I'm afraid I haven't really looked into the cause too in-depth; however, the times I did look, no one seemed to have an answer, including SE Answers on twitter. They just told me my charger might be bad -- yeah that's a cop-out answer for "We don't know", lol.
All I can tell you is that it isn't uncommon. Try charging from a PC, like I said that seems to do it for me.