Much measuring and reading and I have found the problem with my 5000 not charging. Yellow light is on and stays but the battery never charges.
The solution is the component marked with the red stripe. Does anyone have a motherboard out of a 5X00 that they can measure the resistance on. It may be a fuse but if I short it out the current flow through the battery is 1 amp which seems a lot. According to the datasheet sample it should be a resistor of around 19k but the Zaurus doesn't use the chip in the way recommended by the data sheet so it's going to be different.
Sorry for the size of the file, it's 600k but had to be in order to see the componenet I am talking about.