I would stay out of boost until you figure out what is going on. Perhaps go back to stock tune, do a couple pulls and see if you are getting this knock / negative corrections. I think then you can chalk it up to being bad fuel?
I've never had my Octane learn ratio move from -1 once I got it there. I know the general consensus is you can add 1 gallon of e85 to a full tank and that could potentially solve your bad gas issues.
I know with my DHM custom tune even with 11 revisions I still got some negative corrections going to -1 or -2 and some knock 1 or 2 knocks for 1 or 2 cylinders in a 3rd gear pull.
I'm now on the base tune of stratified's e85 tune, and even on the first revision of the tune, I have NO negative corrections, and NO knock. E85 is magic, and 91 octane in California is absolute garbage.