Dealer recalibrated my PDK a few times and that seemed to help.

 

I have also noticed a slight clunking sound between gears 1 and 3 on my PDK. I've had it taken to the dealer several times to try and remedy this problem but it's come back with no problems. The dealer recommends I take a ride with one of their technicians but I only send my car in when I go abroad for business trips so I'm never around when it's actually with them.

 

Interesting as you seem to be the only other person I've found with this issue.
I have a 2011 997 Turbo S and my PDK also made some weird clunk/grind type noises when shifting in auto between gears particularly down shifting and coming to a halt. The dealer here in Dubai updated the PDK software as it was factory settngs. The noise is less prominent but still there. The diff obv makes a noise around corners but the shifting noises are peculiar. Ive compared it to my friends 997 Turbo S of the same year and his seems smoother and quieter. No solution to date.