Controller Hotkey Issue with Livesplits
 

So I recently downloaded livesplits to run while I'm playing games with Project64. I had the bright idea to make map the split and reset actions to the arrow buttons on my N64 controller as the game I want to speedrun doesn't use them. My problem is that while I'm playing, I can't get livesplits to recognize the controller unless I stop.

Does anyone know what is causing this issue and how I could fix it?