I've just done a new design based on MCF52259 and I'm having several issues with it.
I think it could be related with the crystal, but I'm not confident about it.
I've got the very same configuration as in Tower, Demo or Evaluation boards. A Citizen crystal, 48Mhz fundamental, with 16pF capacitors, 1MOhm resistance between pins 1 and 3 and CLKMOD[1:0] are both set to zero with 10k pull down resistors. XTAL is set to 3.3V by a 10k pull-up resistor. As you can see, this is the same that is done in Evaluation and Demo boards.
I've got a simple program which compiles and I program the flash memory with an P&E BDM. Everything works fine, first it erases the flash memory and then programs it.
Next step, I run the program in debug mode. It's just a led blinking and it works fine. If I check the XTAL signal, it has a 48Mhz signal, and the CLKOUT has a 80MHz signal.
Then I turn off the board, unplug the BDM and turn on the board. The program doesn't work at all, and if I check the XTAL, it doesn't have any signal at all, and the CLKOUT has a 8MHz signal.
I'm really confused so any help will be welcomed.