Your using PI to stack correct (post processing)?
If so, when you open your stacked LRGB files three windows will open. The bottom window (first to open) is the one with all your data in it, the other two are the high and low pass rejected data.
I don't know what what constitutes as cutoff data for either low or high passes, but it should be in the post processing area somewhere, i believe it is the Sigma Low and Sigma High values under Image Integration (under Lights).
Mine are set to 4.00 and 3.00 respectively.
Maybe check them and make sure the values arn't funky.
I have seen something similar on my shots using PI to stack. I then ran the data through DSS to stack and it was fine
