So you know, this is with an SL-6000 running pdaXrom rc10 (Kathrin)
I learned the hard way that running "shutdown -h now" on a 6000 might not be a good move at this stage in the game. I couldn't get the Z to start up again. No orange light would come on when I plugged it in either. I did the following to get it to work:
1. Unplug the Zaurus.
2. Take the big battery out of the back.
3. Keep the backup battery switch on.
4. Short the terminals that were connecting to the battery with a penny.
5. Poke the Z with a couple of reset button bushings.
6. Pack battery back in and secure it with the two switches.
7. Plug it back in. If the orange light comes on, you're golden.