Sorry i can't help BUT I have the same problem and question with my T60.
This started last week when the computer awoke out of standby in my briefcase and the charge on both batteries was depleted when i next took it out for use. the main battery then charge to 100% and the spare (in bay) charged to 63% but the orange flashing battery icon has stayed on. Initially the computer would not run w/out the power supply plugged in, but it would restart on the spare battery alone... when it first happened i thought running down that battery might resmarten things but all it did was to deplete the spare to 0% and it no longer is charged it at all, while the main battery remains the same: indicating 100% but is not accessed at all (the power supply is needed to run the computer). Removing and replacing the main battery has had no effect, neither has repeated restarts or power cycling (hard or gentle).
If i unplug the power supply it goes nuts and tries to restart but cycles rapidly between shut down and first powering attempts (inferring there is some charge in the battery but that something is very confused).
I'm assuming that there may be some confused logic or setting in the battery that is preventing it from telling the computer it is "OK & charged", but have found no information as to how to reset or clear the error.