Hi Jared,
A very common cause for "run away" is that you have positive feedback instead of negative feedback. This causes any error to get bigger and bigger rather than smaller and smaller.
You can change positive to negative feedback by reversing anything in the axis. The simplest thing to reverse is the OutputGain.
To reverse the direction of the working X axis: reverse the direction the encoder reads by reversing the sign on the InputGain0 parameter. But since this would cause positive feedback a second reversal needs to be made to keep the feedback negative (two negatives makes a positive). So also reverse the OutputGain.
If this doesn't solve the problem, do a "Move" on the Step Response Screen and plot Command, Position, and Output. Capture the screen as a *.png file and attach it so we can analyze what is happening.
Regards
TK