The BAYERPAT keyword is produced for biases and darks but not for flats. This messes up WBPP processing in PixInsight as a CFA pattern mismatch occurs between darks and flats. Not a big problem but would be much nicer to have the keyword in flats also.
Perhaps your sequence for capturing flat frames is not configured completely? I had the same issue, and it turned out that the bayer pattern was not set in the sequence for capturing flat frames, see Include missing FITS keywords in flat frames .
I re-verified in the code that there is no check for frame type when considering whether or not to emit the BAYERPAT header. The only check is whether or not, for the current sequence, the bayer pattern value is explicitly set. Maybe it’s not? Maybe it’s in your profile and there’s a bug that does not transfer it to the sequence in some cases?