Have a look in the Midi In settings it might be on Omni so it's inputting all channels from the BB piano roll track.
Or you can just use
Element set it to EXT for external sync and don't connect the Midi In.
If you use Element with FL just Save Group once you have it all set up how you want then just Load Group will load the VST chain without messing around.
This is normal with Biab "WORKAROUNDS" it don't work like everything else.