Reading through your comments, I'm wondering...
Midi channels are a specific thing, I understand the point to this. The main point is to separate multiple instruments/functions, so that you can play actual music, i.e. have piano on channel 1, flute on 2, bass on 3, etc.
If your setup has all sounds from one bank as channel 1, and all sounds from another bank on channel 2, then this rather misses the main point. So I'm wondering, do you mean the same thing when referring to 'channels' for Kontakt (this is a soft synth system ??) as you do when referring to midi channels?
Having ALL the sounds available in one bank ONLY one at a time seems somewhat odd? If this is so, then you can play a piece with 2 instruments ONLY, i.e. one on channel 1, the other on channel 2. Maybe with such a setup you could have two - say - pianos on one channel, and say two of another instrument?
OR, do you have to be doing Program Change commands ALL the time, to swap between instruments using the same channel?
I have a different soft synth set up on my PC. At present, it has one SoundFont file set up, although that file contains a number of Banks. I'm not sure how that might swap between Banks, I'll try to check that out. This might touch on the same problem you're having?