I've been testing this because I was trying to use fits formats instead of DNG but the settings are reverted as soon as I take a shot. Attached are the logs.
The K-5II is a BGGR array but is always reverted to RGGB. Also, the image size I'm trying to set to max 3344 but is always reverted to 3264. This happens with both GPoto driver and Pentax driver - also in logs.
The log contains no usable info. Please enable INDI+CCD logging fully (check under Options in the driver tab just to make sure everything is turned on). Also, check your config file under ~/.indi, what's the property CFA_TYPE set to?
If I set the capture to Native, the settings in the control panel are unchanged but when I select fits capture, and do a capture, the frame size and CFA type are changed.
So libraw parses the image and detect RGGB. Can you share the raw image and let's investigate what's going on with libraw? It could be either a bug on our side or on libraw.
I checked the DNG with RawTherapee and it says BGGR so I don't know where Libraw is getting RGGB.
I see that the 3264 is the "declared" vertical image size but full dimensions I believe are 4950x3344. I'm unable to set more than 3264 in the frame size settings in the capture tab, even if I set 3344 in the control panel.