ok...
Either your gear is set up to recieve midi on specific channels, which would mean that when you shift to B, it's expecting data from one specific channel but you've set up the wrong one for the output...
otherwise it's because you need to assign different channels to each gear (no overlaps!) because they recieve midi data on any channel sending. That means that when you go messing with channel A, channel B still gets input.
assign channels 1-8 to A and channels 9-16 to B or something similar...
my guess is that it's the last situation...