Hey Justin,
what scott_ says is on the money...
check the LED indicator on the drive controller and see if it is showing any flash codes. By the way you described the issue though as only temporary (comes and goes) it may not show you anything except during operation.
And as for the controller at the joystick, that is a MIB controller for hydraulics as scott_ said and will not cause any problem like this.
-check your directional and 1A contactors and their tips
-does the drive motor have a clicking sound when driving the machine?
There is a reason i'm asking about the clicking sound...
These motors are pretty good motors but cannot stand much abuse and if they are stalled very much the com bars on the armature can raise up slightly and when they pass by the brushes they will click. If this condition is bad enough it will be fairly loud, when this happens that can make the brushes jump off of the armature commutator and can make it fault out but not remain in that condition if the power is cycled, drive function returned to neutral and then reselected. I have seen this happen many times in these units and others before.