I just released a new firmware version which adds support for 'MIDI2 for Sysex Only' (MIDI2ForSysex) on STM32 based MegaDrum. When MIDI2ForSysex is set to Yes the second USB MIDI Port will transmit only SySex messages. Default is No. This is implemented to prevent MIDI softs/synths listening on all MIDI ports from receiving the same Note On/Off messages twice.
This new firmware version is acompanied by a new MegaDrumManager version, 20150110, which adds support for 'MIDI2 For Sysex Only' (in Global settings).