The Ha (as well as the others) definitely haven't been flattened. I was using new Astrodon filters I recently got and haven't had time to run Flats for the filters as yet, so it was all processed with only Darks & Bias I had done for the camera. I'll give a shot at reprocessing the Ha data though to see if I can clear up the walking noise you mention. Only had about 10 frames (at 2 minutes each) for each filter (Ha included), so not a HUGE sampling to draw from overall. 100 minutes total for everything.
Edit: I ran the BPP for the Ha at Averaged Sigma Clipping (since there were only 10 frames) and tried again with Winsored. The new one might be a little better, but hard to really tell. Would another method really help better given the limited number of subs? Or just need to change some of the Image Integration parameters in BPP? Overall it seems like I definitely have more there than I can use, just a matter of figuring out how to get it all together and then processed. Gonna hunt over the holiday and hopefully I can find all my notes again. Hate having to start from scratch. Heh.