This can happen if your host software is routing MIDI data from the ReMOTE SL Port 2 or 3 into the plug-in when you are using Automap Universal, and the plug-in responds to the particular CC or NRPN message that the control uses. Port 3 is designed to be used exclusively for communication with the Automap Server, and Port 2 is used by the Mixer automaps, so please consult your host software's documentation to find out how to prevent MIDI data on these ports being routed to MIDI tracks in your sequencer.

All communication from the SL is on MIDI channel 16, so if it is not possible to disable particular ports in your host software, at least try to avoid this channel.