Sounds very similar to the issue I was having myself. It was a long time ago and I don't remember clearly, but I remember doing something along these lines to fix it:
Move the file called "ignoreportfilter", found in a folder that should be called (or similar) "c:\program Files\Steinberg\Cubase\MIDI PortEnabler".
Move this "ignoreportfilter" file up to the main directory "c:\program Files\Steinberg\Cubase\".
Also I tried playing around with disabling "emulated ports", plus the timestamp settings, but from memory it was moving the "ignoreportfilter" file that helped.
Good luck!
P.S. I doubt it's the through port on your controller.
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