Craig,
I glad to hear that the FLAT compensation in CaLIGHTs solved a problem for you. CaLIGHTs uses your masterFLAT and (masterDARKFLAT or masterBIAS) to establish a 100% flatfield compensation. Clicking on the 100.0 multiplier value causes a calibrated image of your highlighted image in the LIGHTs list. There is a FLAT Comp Multiplier slider that can be adjusted from 0%=No FLAT compensation used all the way up to 200%=Double the FLAT compensation. I have had to use this a couple of times with success.
Using a value more or less than 100% implies that either your FLATs and/or your DARKFLATs or BIAS frames are not ideal. My observation is that some people take FLATs that are very dim...less than 20% brightness. The dimmer your FLAT frames the more noisy and problematic FLAT compensation becomes. The important detail that led to my current practise is that your FLATs do not need to be at the same ISO or exposure as your LIGHT frames. I use an LED light table and take my FLATs while the sky is still darkening. I also use the minimum possible ISO/GAIN for my camera and set the exposure so that I get pixel ADU values that are close to 75% of fullscale. With the LeNhance narrowband filter and my 80mm Refractor, II use the maximum brightness on the LED light table and exposure of roughly 1.5 seconds. This gives me pixel values peaking out at 76% of maximum. My QHY294C camera is very linear, as are most of the modern CMOS camera so 76% is OK. SharpCap's sensor analysis says my camera has a linearity > 95%.
Using 76% ADU at the lowest GAIN for the QHY294C represents a huge number of collected photons and the more photons collected results in higher SNR in my FLATs. All this means is that with 10 or 15 FLATs I can achieve a very high quality masterFLAT with extremely low noise. If you want to read more about my LIGHT table solution use this link.
Peter