I still haven't figured out why the normal timer interrupts were not working, but I did manage to get the sleep timer to work (which is what I needed anyway to pull the chip out of low power mode).
The problem was that a timer compare event throws an interrupt, but does not reset the timer (which I was assuming it would)...and since it is a 24 bit timer running at 32 kHz, it takes a very long time to roll over and hit the old set point again.