As mentioned by f3racer, out of the box, the power commander unit is at a "zero setting" with no changes being made to alter air/fuel ratios.
The act of altering the base setting via importing a saved map or creating a custom map via a series of dyno runs is what alters your fuel metering.
These bikes generally don't care much for putting below 3500 RPM, and especially below 3000 RPM (Harleys they ain't).
At low RPMs and in lower gears (3rd or below), they can easily get into very jerky or lurching motion through a combination of flywheel inertia and multiplication of force by the lower gearing selection.
When that occurs, I usually just grab the clutch lever, disengage the engine, and let it settle down.
Above 4000 PRM, no problems with mine in any gear.
Now if it's misbehaving while traveling down the freeway, and it has an aftermarket exhaust, the exhaust may be causing a lean condition at certain RPM ranges.
When I first bought mine, it had a Jardine 2 to 1 exhaust installed, and beginning at 5600 RPM, it began getting really lean to the point of misfiring.
A simple dyno run to remap the power commander and everything was just dandy.