USB3 doesn’t always work with older USB devices even though it’s “backwards compatible”, I’ve had problems with other USB devices not working correctly on USB3 even though they show up in the OS they aren’t usable like...
Or you could use an external circuit that greatly reduces the bounce that affects encoders. I’ve had great success using this circuit from Bourns and I haven’t missed any steps as far as I can tell:
From looking through the manual, it’s likely this setting here that makes it not recognize the Teensy correctly when there’s more than one port.
This should be set at or above the max number of Teensy usbMIDI ...
usbMIDI.Start will not accomplish what you are looking to do, there is a standard that most DAWs as well as keyboards use for transport control called MIDI Machine Control, I know these work in Reaper and Cubase (Pro...