Sounds like the transport MIDI CC thing. The BSP transmits a MIDI CC when you press stop/play and record. If you synth has any of these assigned to a parameter, it will change the patch on it. To remedy this you will need to connect your BSP to MCC and go into Device settings. Scroll down to the transport setting and either change "Transports" to "off" or "MMC", or change the Stop, Play and Rec Channels to all send CC 124 (omni mode off).
Hope this helps.