1. You need to do Compare Against > Game Time to make sure you see it properly
2. Edit Layout > + > Control > Manual Game Time
3. When you do runs, a little window will pop up with a text field in it. Every time you want to split, type in the IGT number into that window, then press Enter. Your normal split hotkey will not register the game time.

RTA will be timed according to when you press Enter on your IGT window That's it! Happy running :D