So after a bit more troubleshooting, it seems if I take clock/start stop off of omni send, the behavior does not persist. I did not go though each channel to see which one is affecting the MXB global controls as of yet.
I reburned the firmware to make sure it wasn't an issue with my installation and the behavior was still present, so if others can produce, this is most likely a bug.
Perhaps someone smarter than me could exploit this bug for some added midi control? Maybe there are other back door entrances to programming the MXB via midi we have yet to find?