Campagnolo Record C9 / Shimano CS-HG200-9 incompatibility
Might be a spec change by Shimano - I know that there is no change to the Campag chain. As they are not designed to be compatible, if Shimano have changed something they will have done so only referencing their own 9s HG type chain which is slightly narrower than Campagnolo's.

The other things to look at are a stiif link or a chain rivet protruding slightly at the join.

If it's once per crank rev (rather than once per full chain rev) it would be more likely to be related to the rings - if you are doing 11000km per chain / cassette I'd guess the rings might be getting pretty tired unless you are changing once every couple of chains - depends whose rings, riding conditions etc ...