i read through that discussion on google's forums, and this was one thing that jumped out
It is more likely something to do with conversion rate of the clicks generated through your site.
as far as i know google is not doing pay-per-action, its always pay-per-click, but i did hear someone say once that they were ignoring genuine clicks if the user immediately pressed their back button. because its a poor return for the advertiser. maybe it's something to do with that.
it might be something to do with your ads subject matter. if people are clicking the ads only to find that the resulting site is not what they want, a high percentage of them could be clicking back quickly. presumably google would then discount the clicks.
there is also one obvious thing, which i'm sure you have already checked... but is it possible that you've not got your site (or one of your sites) listed in the "allowed sites" box? google might be ignoring a load of clicks for that reason.