Your process should be to calibrate using your master frames and then use the Cosmetic Correction process. Then align and create the master light frames. Make sure you use the proper combine method depending on the number of frames you have. A guideline posted some time back was Percentile Clipping for up to 6 frames, Sigma Clipping for 7-10, Averaged Sigma Clipping for 10-14, Winsorized Sigma Clipping for +15, and Linear Fit Clipping for 25+.
I tend to use the default settings under Pixel Rejection (2) and always use Average for my Combination method. At least this is how I do it.
-Steve