It could be the BME is acting flakey, try doing the BME reset as the BME thinks it knows your capacity and might be acting wonky or has an error value.

It does NOT sound like the broken USB issue( I have had this with 2 N900s) as nothing will happen at all except maybe when you wiggle the cable right, and that only the first few times.

BME re-calibrate:
-In terminal type(dont remember if you need gainroot or sudo, I think not)
Above saves lot of frustration with getting completely BS values posing as correct, when battery gauge is not calibrated (at all 0 like, lost calibration data due to battery out of device for too long and dead bupbat).

-Reboot
-charge to green light
-let run until battery dies(battery is now calibrated, dont rush or you will end up having to redo, last few hundred mA should be spent with backlight , CPU, and things like WiFi off)