Turns out a program change message CAN reset the channel strip. From the Logic docs:
"You can remotely switch between channel strip settings by sending MIDI program change messages. This allows you to select your favorite sounds by pushing a button on your MIDI keyboard. To use this feature, you need to save a channel strip setting as a performance."
Also turns out I had a few settings saved as performances (meaning they were saved into a folder called Performance, inside the Instruments folder for saved Channel Strips), certainly done out of ignorance, including the problem one. And removing them all has fixed the problem (and revealed some possibilities). So, not so tough after all:)
But it also seems pretty clear that this means there is a MIDI program change message tucked away in the OM Preference settings for Bus 1, doesn't it? If so, I wonder how to edit it?