Those two extra cables connect between the tow unused connectors on the TE2+ EZ MOD and the Brook UFB. One is for future touchpad support (if they implement) and the other is the DP/RS/LS connector.
It sounds like the EZ MOD is working fine, but the Brook UFB is not. My board routes signals only and doesn’t touch the USB lines whatsoever. That blinking light on the EZ MOD is a “heartbeat” that shows the code is executing in the EZ MOD that handles all of the Player LEDs, etc. Things that need some sort of processing to work with the Brook basically. All inputs like start, home, select, DULR, and the P1-K4, are simply passed right to the Brook. So if its not autodetecting, its an issue I can’t fix.
Try using the USB output on the Brook UFB with a USB cable and see if the situation is the same.