We are seeing the same on RB1100ahx2. Port 11/12 seem to be fine but ports on the switch chips are unusable.We're seeing the same problems: in rb1100ahx2 some ethernets simply won't go to full duplex (even if auto is disabled).
recycling the interface(disa>ena) won't help.
Although officially not required, some manufacturers recommend a minimum cable length of 1 meter.. You can try using a longer cable.This specific ethernet is in a 15cm stack shielded cable to the fiber company router.
No way it's the snr in the cables, or EMI, cause it's fit in a #14 steel outdoor rack. The ethernet is locked ad 100FDX, but gets stuck at 100HDX in 6.3 firmware(HOW? both devices are locked at 100FDX!!).
Solution: went back to 6.2 and everything is working properly.