Searching this forum I found the thread on pulsating fan http://forum.thinkpads.com/viewtopic.php?t=27245. The fix was to re-solder an inductor on the reverse of the board. So after looking near the battery connectors, I found another one of these problem inductors where one of the solder joints had broken. Re-soldered it and now the battery charges normally.
Thought I would add a post for reference.



