maybe this will shed some light on your problem, OP.

i've recently had a similar experience in adjusting my headset. i suspected that the crown race was not seated properly on the fork. there was always a slight clunk when hitting small holes in the road. i checked everything over the next few rides, hoping it was a clicking brake lever, or brake housing, or loose skewer. i could feel no looseness in the headset and had adjusted it a number of times. i figured if the crown race was not seated completely, a few hundred miles of bad road might make a difference. anyway, last night i was at it again, after a riding the bike, and noticed that i could create a clunk by just hitting the front tire, hard, towards the rear of the bike. i figured it had to be a loose headset. so i tightened it down to the point where there was a bit i tightness in it, then went for a ride. there was no noise on the ride and no tightness in the headset after the ride. i figure the crown race wasn't completely seated.