Technically for RJ45 its mandatory to use autonegotiation according to IEEE standard.
So that should NOT be disabled.
Also with autoneg disabled the auto mdi/mdix will also get disabled so you are then down to use the correct cable like a straight cable between your device and a host and a crossover cable if you connect your device to another router or switch.
If you scroll down in that settings page how is advertised being configured?
I assume you have tested this particular transceiver and cable in another device just to rule things out that its not broken on its own (or for that matter whats on the other end of the cable is broken)?
Have you tried plugin the transceiver in another slot?
You seem to be trying sfp2, have you tried putting it in sfp12 or such (thinking of the issue with port 1-8 on CRS354 switches in case something similar is going on here)?
You can also try to set the rate-select to low and reboot the device (while you are troubleshooting anyway):
http://forum.mikrotik.com/t/special-settings-needed-for-xs-31lc10d-and-xs-2733lc15d/169749/1
http://forum.mikrotik.com/t/sfp-rate-select/152511/1
Also what version are you currently using?
Try to boot into 7.16.beta4 testing to see if there are any changes?
Edit: That port 1-8 issue on CRS354 seems to be related to the PHY itself if its just bad soldering on a batch or something like that.
Shouldnt be the case in your case since the CCR2216 use a single phy as it seems according to the block diagram for int1-12:
https://i.mt.lv/cdn/product_files/CCR2216-1G-12XS-2XQ_220346.png
If you compare with the block diagram for CRS354:
https://i.mt.lv/cdn/product_files/CRS354-48G-4Splus2Qplus_200122.png
But its still worth and easy to test just put it in another slot as far away as possible from the current slot.