All devices are made by Mikrotik, so I suppose they should be compatible. Mikrotik RBGPOE injector is made for 1Gbit connection and it works with Mikrotik wAP ac on 1Gbit…
I see that both sides are reported as advertising only up to 100 Mbps as possible on this, have you tried to run a cable test from each device across the cable when its not connected at the other end to ensure there is no breakage or anything weird? Have you tried another RBGPOE? Also have you checked the interface configuration to ensure the port isn’t set to only negotiate up to 100Mbps?
Never rule out that a cable or adapter could have gone bad, never rule out an accidental button click. So many things could contribute to this.
Also check that you have updated routerOS to the latest version (any of the latest chain releases) and also check that you have updated to the latest routerBoot. There are a number of changelog entries in routerBoot changelog that talk about ethernet interface funny things and newer firmware often mentions improvements to link auto negotiate.
I know you mention it works through unpowered RBGPOE, I would test an alternative one of those and also try a different power supply plugged into it to ensure the power supply isn’t noisy or shielding failure on the POE injector.
Replaced all wiring, also got rid of RBGPOE and replaced it with RB260GSP(two wAP ac and RB260GS powered by it). Problem somehow solved and now all connection is at 1000 Mbit.