FLStudio or the plugin is the first to respond to keyboard shortcuts. When selected - The plugin uses keyboard shortcuts before FLStudio. Any unused shortcuts are passed onto FLStudio. When deselected - FLStudio uses keyboard shortcuts first then ...
FLStudio will look for the FLStudio engine. Normally this is the location of FLStudio that was most recently installed. You may want to use another installation of FLStudio, for example an Alpha or Beta for testing ...