Yes, but on that thread, once the MTU/fasttrack issue was solved, the OP was happy with the device connected to his Hex S, this should mean that there is not a “generic” incompatibility issue between Mikrotik and that Zyxel SFP, which leaves us with:
- a specific incompatibility between your CCR2004-16G-12S+ and the Zyxel PMG3000-D20B (possible but IMHO improbable)
- something in the firmware or settings of the Zyxel PMG3000-D20B (what you are suspecting, most probable)
- something in your Router OS settings (less probable, still possible)
For #2, I don’t think you will find many people with Zyxel experience here.
For #3, if you post your configuration, following these instructions:
http://forum.mikrotik.com/t/forum-rules/173010/1
some of the more experienced members may be able to review it and possibly spot something that might be involved, or however give you some instructions on how/what to log on the Mikrotik side.