Hey everyone,
I'm having the same issue as described above. OSX is showing 3 I/Os and 11 outs. So far I have done the following:
updated the firmware on the rk006
followed the instructions here/in the YouTube ideo on the RetroKits YouTube channel
updated OSX the the very latest version (Sequoia 15.0)
used the factory reset long-press function on the device
When I enable the USB quirk mode on the RK006 it shows as having one port, essentially an all port that sends to every midi out on the device. When I revert to the standard setting I get the same odd behavior of some outputs being "all" and others not corresponding to their logical port etc, etc.
I will submit a bug report to Apple, but I thought they had solved this issue?