I think the fits warning is normal. Pixinsight tries to push you to use the xisf file format over fits for the reason described in the error you got.
If you are trying to calibrate with Cal frames captured with a different tool than ekos the incompatible geometry error can happen. This has to do with how different drivers read out the camera. Try grabbing some Cal frames within ekos.
The following user(s) said Thank You: Jasem Mutlaq
This is interesting.. I wonder if this has to do with the FITS data read as top-down or bottom-up. Can you please open this same topic in the PixInsight forum and I'll follow up with you there?
Regarding the geometry error - frames pulled via indi w/ Ekos and other clients (PixInsight included) are definitely different than those captured with TheSkyX on Linux (incl RPi) for at least the FLI drivers. As an example I get overscan margins w/ indi but not with TSX. It's probable that other cameras are similar. I wouldn't be surprised if this is the case.
PixInsight will error if the image geometry (matrix size, possibly pixel depth too) is not exactly the same between the calibrating frame and the frame to be calibrated - they can't line up.
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.