Daniel, while I don't think that your tank issues are specifically due to the change to AF salt, I would feel bad reccomending you change your established system now, especially if you had additional issues. I hope you understand.
I myself haven't had the bacteria to dose for over a week and my system is doing very well. I wasn't paying close attention to the amount of ProBio S I had and ran out, and it was back ordered so I won't get it until this week.
I'm a huge believer in the system but I think it's best to go with the carbon source, bacteria, and strong skimming at a minimum rather than setting up a hybrid. I'm hoping your tank continues to recover and I still scratch my head at what could have exactly gone wrong. If you saw some of the crud I've put my tank through without having issues you would see why it baffles me. The only time I had issues like you are seeing was when I ran Zeovit. Random bouts of STN really tested my devotion.:headwally: