I don't have a solution, but I have some questions.
The MCG in this chip has an FLL and a PLL. Has anyone seen anything describing WHY you might run with one or the other? What can one do that the other can't?
Searching for "MCG PLL FLL" on this site brings up a lot of matches. Have you found anything useful in any of them? This one looks interesting:
I've been looking for relevant App Notes, but can only find ones like this for an S08. It details the IGC and the MCG, and says when (and how) to use an FLL vs a PLL:
http://cache.nxp.com/docs/en/application-note/AN3499.pdf?fsrch=1&sr=3&pageNum=1
Are you following the "permitted mode transitions" in "7.4.2 MCG Mode State Diagram"?
Can you try and lock the PLL to the Crystal and maybe not upset the FLL as much?
Tom