I got to the root of the problem. The first partition on the 2G SD was formatted as FAT32, but maemo wasn't detecting it. When I went back to the factory default OS, it was going crazy trying to detect an SD card. Strangely, the external miniSD was untouched, but the system gave up on mounting it after it could not talk to the internal SD card. I think some of the default apps need space on the card to write their cache and other data, and was spending more CPU cycles. /proc/loadavg was constantly above 4 which can explain why the battery drained faster. There was a mount in uninterrupted sleep (D on ps wwaux), maybe shutdown froze trying to kill it.

I cleaned up the internal card and reformatted as ext3, and was good to go. I wish I had got some good indication that the OS was spending CPU cycles because of it.