I have adapted code for the K40 tower running in PEE mode at 96MHz. (from an external 8Mhz xtal) this is confirmed by register settings checked in debug and a correct baud rate on serial port. The freq of MCGOUT = system clock = 96Mhz. I measure 48Mhz on a scope at the trace output.
Does the trace output do an (undocumented ?) divide by 2?