I don't really have a great answer for you. But I took a closer look at the behaviour I see with my camera.
My RAW images are supposed to be 5184x3456.
When set to FITS, the viewer tells me the correct dimension.
When set to Native, The viewer tells me 5202x3465. However the RAW files actually are 5184x3456 in Photoshop.
If I open an external image that was captured with just the camera normally, It comes up with 5202x3465 in the FITS Viewer.

Curiously, DeepSkyStacker also shows my raw image files are 5202x3465. But a FITS image is still 5184x3456 DSS. Because of this I can not use dark frames captured in RAW format with FITS lights.
It probably has something to do with debayering.

I think your settings probably kept resetting because you have a sequence in the queue made with those values and they are being written back to the driver when the sequence runs. That will change the frame size in FITS mode, but not in Native.

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