jwake2
Hi, jwake2!
The principle of saving fit and tif is not to modify any of the original data, so stretching does not take effect. The reason fit looks like it works is because it automatically stretched during preview, but tif doesn't.
The principle of saving JPG and PNG is what you see is what you get.
For your question "Stacked Lights and Darks looks GREAT in the program display, but the saved Fits files are way too red or blue depending on which bayer I select." is that the image displayed in the program has undergone white balance processing.
No jpg saved is that you did not click the save button.
We will provide more save options in the future. Thank you for your support!