While it looks like a hardware fault, it could also be the embedded controller/charge controller being in a undefined state. While this would probably also be just a coincidence, there might be malware interfering with the embedded controller. Your removal steps (which are unknown to us) might also have had an impact.
To restart the embedded controller, disconnect power supply, remove battery an try to power on the laptop. This obviously will not work, but helps to discharge capaciators powering the controller. Then reinsert battery and connect power supply again and see if it begins to charge. If not, the controller might have been running without interruption despite of the power-on attempt. In this case repeat these steps but wait some time (maybe one day) before reinserting/connecting.
1Do the batteries charge when the system isn't on? If so this has absolutely nothing to do with the software and is just a coincidence. – Shinrai – 2012-05-18T14:13:50.657
@Shinrai You mean "if not"? Because if it does charge when off, then it is likely software related. – Bob – 2012-05-18T14:23:45.513
2@Bob: I think you misread Shinrai (or a comment edit beat you), though it is a bit convoluted in negations, so it's understandable :-) . "If it charges when turned off, then it is not related to software." – Daniel Andersson – 2012-05-18T14:28:29.880
1the laptop battery does not charge when the laptop is powered off and plugged in – Nathaniel_613 – 2012-05-18T14:36:00.817
@Bob - I did mean 'if not'. – Shinrai – 2012-05-18T14:50:41.267
FWIW, after a Windoze Vista update several days ago my battery charge icon does not animate correctly, though it still seems to charge OK. – Daniel R Hicks – 2012-10-19T01:45:09.063