There's the obvious question of what's under your S21 - is R24 installed?
For just one other instance - J92. Details like jumpers are important.
I doubt R24 is installed on mine, otherwise the DIP switch #4 wouldn't do a thing. I did try switching it on, with the scope attached, and the signal did not change.
J92 is maybe something like a test point, or designed to be closed. I don't see a guide/pilot on that, so I think it's really a jumper and not a socket for plugging something in. But anyway, it's not closed on your board either, so it's not it.
Do you know what J72 (ACLK) on your board is for? Mine doesn't have this.
And don't simply "assume the firmware is to blame". Personally, I assume that the firmware is not to blame.
You asked for clues. Please let us know how the wind is blowing.
You're right, of course, should not assume anything prematurely. The wind was good, I broke the nose on my board =)
I'm getting back in 2 weeks and will disassemble the ISS and get better lit pictures of the board, both sides. I can't really remove the board from the station, because the antenna is soldered to the board and it and the antenna cable doesn't detach from the antenna.