I don't think he means the footswitches, I think he means the per-scene MIDI PC assignments.
I have had trouble with the MIDI PC in Scenes 5-8 as well, but only in AX8-Edit. It always shows "Off" and Channel 1, even after saving with different values, leaving the preset, and then returning to the preset. So, when I need to send MIDI from Scenes 5-8, I edit those values on the unit itself.
Seems like a legit bug, maybe @Michael Pickens can take a look?
What I've noticed is that adjusting the settings for 5-8 in AX8-Edit works (a message is sent when you set the setting), but it doesn't save. It's been this way for awhile, I just haven't ever mentioned because I rarely use that many scenes.