What happens if you calibrate a few flat frames with the master flat, Chris? If everything is working as it should that will give you an evenly illuminated result with no visible structures.
If you still get bad results then that points to a problem with capturing and/or creating the master flat. If it works, then that points to some sort of compatibility issue between flats and lights.
A bit of the old divide and conquer...
Cheers,
Rick.
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