And what's more, the flats and darks do not give me: ** Warning: The FITS format does not define an unambiguous orientation of pixel data. The coordinates read on the image may be wrong.
So it's just the lights that seem to contain the unambiguous orientation data.
My lights are also RAW16 so they are not debayered. But I think that is not the point. PixInsight doesn't seem to be able to unambiguously determine the orientation.
Could it be that there is some information added in the keywords that causes this?
Isn't it the same size as the light frame you attached to the post? Unless you mean the stacked masterflat.
A single flat frame would be just fine to inspect this issue. This way we can look into it and help.