tl/dr MSP isn't reading gains from stagebox channels above #35.
Troubleshooting this one was fun. Qu32 to AR2412 to AB168. I usually put the AB168 upstage, but patch it in the low channels. I just built a scene on the board. When I open MSP, CH12-16 all show gain 5, which should be 28. They're patched to Expander 12-16. I reset all the gains to see if I could figure out what it was reading where. CH32 is local, and I set its gain to 60. I set the gains on Ch1-31 to the values 1-40, matching the stagebox channel they were patched to. In order to do that, I had to pad the first 4. This uncovered another bug, which I am also posting. Since the channels I noticed were displaying 5, I set the stagebox 5 channel to padded 5, in order to differentiate it. I saved that scene, quit MSP, and reopened MSP. All channels displayed as expected, except 12-16, which displayed 5. I also noticed that they didn't show phantom power on, although it was. It looks like MSP is not loading preamp data for those 5 channels. I went back through some older scenes. Another missed Extender 12-16. 1 loaded every channel except 12, which was patched to Extender 12. Extender 13-16 weren't used.
So, in summary, I don't think MSP is getting preamp data from Extender channels 12-16, which correspond to channels 36-40 in a straight patch. If I patch those preamps someplace else, the bug follows them.
I am pretty sure I've gotten bit by this one on my GLD, too, but I didn't have time to dig into it.