When a scene is applied, Forte first updates the plugin's data (FXP, FXB, params, etc.)  After that it may send various optional MIDI messages like All Notes Off (which sends CC123 and CC64=0), All Sounds Off, Reset All Controllers, and program changes.  It is up to the plugin how it reacts to these MIDI messages.  For instance, the Arturia plugins can interpret the CC64=0 as an instruction to turn off the "Release" button on the synth.  

The fix for problems like this are to turn off these Scene Command options and update the scene(s).