Diagnosis
It's not broken, it's just badly out of sync. This happens if the legs weren't at roughly the same starting height when you plugged everything in for the first time.
How to Fix It
Unplug the desk. Manually crank both legs down to their absolute lowest position. There's a hex key hole on the end of each motor (under the plastic cap on the foot). Use the provided Allen key to turn them clockwise until they won't go any further. This physically resets the legs. Plug the desk back in. Now when you press down, they'll start in sync.
If That Didn't Work
The synchronization data in the control box is corrupted. Hold the 'M' and down arrow buttons on the keypad for 5 seconds until it beeps. This performs a full motor reset.
Heads Up
Never use crank while the desk is plugged in. You can strip the gears or blow the control board.