If you have an aux switch connected to the Omniport, it is likely that it is a Normally Closed (NC) switch. The MCx requires a momentary Normally Open (NO) switch. If a NC switch is used, the MCx will read it as a switch being pressed down, which makes it seem like the controller has hanged.
Also, your controller may hang due to an infinite MIDI loop, which happens when you have the MIDI signal connected back to the controller MIDI Input and have MIDI Thru turned on. Thus, when you send a MIDI message, it travels in an infinite loop and will cause unexpected behaviour.