Hi Paul,
For PGE board, the Flexray clock (should 80MHz) is from FPLL (configured in PLLCTL3, 0x0040,0900). Configuration PLLCTL1 to 140MHz HCLK doesn't affect flexray clock (80MHz).
Can you please try 1 MDK board, 1 PGE board, and 1 PC card? What is the termination on your PGE board? The Flexray spec defines that the minimum DC load is 40ohms. If the DC load of your FR network is below this value, please change the termination of your board, or just remove the termination on your PGE board.
Regards,
QJ