Cura has a profile for The Makerbot Replicator and allows you to chose between 3 types of 'Gcode flavors' :
RepRap, UltiGcode, and Makerbot. Lol.. Upon posting this reply and looking at the settings for a referance, I see now that it says "requires MakerWare to generate to X3G"
So.. Thanks for inadvertantly helping me out. It's a bummer that I can't use Cura on its own, it is a far smoother program than the very slow ReplicatorG.