I imagine you have ran into a problem with uneven illumination or gradients in some of your images, and sometimes those simply will not calibrate all the way out with flats.
One a post a couple weeks back I had someone ask about weighting the Ha channel with a multiplier since I mentioned that I did that in processing the image I posted, so here is a quick post showing how to do it in APP and
Deconvolution is one of PixInsight’s most powerful programs, but it is also one that takes some time to understand how to effectively use it, especially for beginners to astro image processing.