Hi James, I wouldn't think that fitting an alternator would cause this problem, Has the alternator got the 2 pin D type plug (flat on one end and curved on the other) If so the 2 wires are only D+ which is warning light and DFM which is field neg terminal which goes to the ecu, the ecu can then earth this terminal if it thinks the battery needs more charge. Could the old alternator have overcharged and caused damage or could someone have tried to jump start the vehicle and got the leads on wrong. ??