Maybe you can also try another experiment, that is to upgrade to 7.23beta2 7.22.1. With that update, EEE is disabled on the RB5009 (the fact that EEE was enabled on the RB5009 in all previous versions is apparently something that MikroTik did not intend, see Page Comparison - Ethernet (v.80 vs v.81) - RouterOS - MikroTik Documentation).
EEE when active is known to cause a lot of connectivity issues (with many kinds of network devices/adapters, not specific to MikroTik or the RB5009).
Update: Fix is now in stable version 7.22.1 V7.22.1 [stable] is released!