Hi, thanks for the report, and glad to hear you found a workaround.
I played around with AAI a little bit and it seems to me that, for some reason, when the AAI transmitter GUI is opened, the transmitter entity will get moved to the same logistic network channel as whatever normal logistic entity was last opened before it (roboport, logistic chest, etc.). So for example, if I open a roboport on channel 1, then close it and open a transmitter, the transmitter will get set to channel 1. If I then open a logistic chest on channel 2, close it, and then reopen the same transmitter, now the transmitter will be on channel 2.
I also noticed that even though the AAI transmitters and receivers show logistic network channel info on hover, they don't seem to allow editing of the logistic network channel when their GUI is opened. This could be part of the same issue... the editor GUI is shared between all entities, so my hunch is that whatever logic error is causing the editing GUI to not open, is also somehow causing the channel to get set to whatever value the editor last held.
I will take a closer look at the issue when I have the time.