(A note to mikrotik employees: the cause of this seems to me to not be a configuration issue so I've filed an official support request as SUP-38183, previously SUP-35938. The request has been unanswered for over a week so I am posting here.)
I've got a CRS328-24P-4S+ with 4 suspicious ports. I've updated to 6.48 and "/system check-installation" passes. Nonetheless I see < 1Mbps in iperf3 tests between two systems connected using ports 9, 10, 11, or 12. I have reset the device to stock configuration.
Attached is configuration detail and test summary. The two systems I'm using for the tests are named nt-1gbaset-c and nt-1gbaset-d. I execute the throughput test detailed at the top of the document, then move ports as indicated per scenario. You can see that when the systems are in ports 9,10 and then in 9,18 bandwidth is significantly reduced. Full bandwidth is restored when the test is run after moving to ports 17,18.
Does anyone have insight into the cause of this problem and resolution of it? Thanks.