Diagnosis
That's usually the crossbar shifting. The bolts connecting the center crossbar to the two feet can work loose over time, creating a small gap. The initial motor torque slams the metal parts together—hence the clunk.
How to Fix It
Unplug the desk. Get under it and locate the four large bolts (two on each side) where the horizontal crossbar attaches to the vertical feet. Tighten them firmly with the provided wrench or a socket set. Don't just snug them; give them a good, solid turn.
If That Didn't Work
The noise could be coming from inside the motor housing. Listen closely to see if it's from one specific leg. A failing motor gear can make a single loud pop on engagement. If it's isolated to one leg, that's a warranty claim.
Heads Up
Periodically check all frame bolts every few months. Vibration from typing and motor movement can loosen them, which leads to more noise and frame stress.