FTL does not affect the HOTKEY you use, just what is SENT to other windows. If you press Shift+R, it will not activate a "R" hotkey in ISBoxer (in WoW it would).

I would have to see your config to tell you what you have bound to Shift+R. The closest thing by default is the repeater toggle Shift+Alt+R, there isn't anything that would block Shift+R unless you made it