Not that anyone cares, but I nailed down exactly what was causing the ego to ignore my keyboard input to stop.
When calling a setMotion the ego will walk just like you pressed a key to make him/her/it walk. However, when asked to stop with keyboard input the ego will ignore your first key press.
When calling a setMotion on the ego it's also necessary to notify it that it's moving in that direction: "(User:prevDir(RIGHT))". This way when you press a key to stop, it will know to stop with a single key press.