Yes, I also checked R109. Although it is common with the rest of the keys, I suspected it could be also the problem because of the forward drop in the diodes (supposing there was a weaker pullup also in the FPGA). But no, it's OK.
Although I had already checked them with the multimeter, I also resoldered relevant pins of U2 (1, 2, 9, 10, 11) and U1 (3, 4, 5), but no luck.
If it's not a SW or FW problem, I can only suspect bad U2, more remotely, bad U1, or, even more strange, a failure in the FPGA section in charge of reading the keyboard.
If I had a longer ribbon cable, I could also try some "live" measurements in the user interface board, but I don't have it.
Unfortunately, without the encoders, the scope is practically useless, but maybe I can still use it with the Keysight application