The shortcut ctrl+r is multipurpose, in the sense that when the queue window is focused ctrl+r will reset the selected failed transfers, now when any other control in the window is focused ctrl+r will function to send a raw command. Off hand I am not sure if this is a oversight or the intended behavior, typically commands do not share the same shortcut, however we are quite limited when it comes to simple shortcuts.
When assigning shortcuts to custom commands we do not recommend overriding any application shortcuts, ctrl+w is used for toggling synchronized browsing.
I suspect that the behavior of the shortcut is switching between the custom command and the application shortcut depending on which one is allowed during the current state of FlashFXP.
I would recommend assigning alt+key or alt+ctrl+key for shortcuts used in custom commands.