I also have same problem "CSS Protocol Plugging: Unknown Protocol Error" when using MC56F8006DEMO kit either with parallel port JTAG or USB TAP adapters, but problem does not appear when I use MC56F8013DEMO kit:
This lead me to think the problem is something related to MC56F8006DEMO kit or MCU, but I can't find some app note about this issue.
¿What should I do to put this demo kit to work properly again?