I've seen this when the 2.6.x kernels were being developed. In my case it was that the CF card was not being shutdown.
Do you have a CF card in the machine? Might be worth taking it out and seeing what happens.
What kernel version is this? There was another glitch during the dev of 2.6.x to do with battery level reporting (depending on whether external power was plugged in when you rebooted of all things ). This meant that the kernel thought the battery was flat, when it actually wasn't.
Si