In SX Microcontrollers, SX/B Compiler and SX-Key Tool, George Herzog wrote:

Also, I just wonder if there is any chance that it would run better at 3.3volts.
One could change the regulator.  It certainly lowers EMI spikes which might contribute to the problem.
Of course that lowers the BOR42 to BOR27 which may put you back into difficulties.

If the TTL crystal and the SXKey both clock the board at 50Mhz, it would seem to not be the board in particular.
Maybe an impedance mismatch with the Murata.  There is a place to tweak it with plugging in capacitors.
You would likely need a scope to get things right though.

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