Almost all affiliate marketing networks (using various reasons, actually excuses, for time to time) do and will keep on doing some "shaving" off from affiliate marketeer's earnings. This is a reality and the only solution to this is to allot some of your profits made into a "shaving off" bucket.
I allot 12% based on my experience, so around 12% of my affiliate earnings get shaved off and it does not affect my expected calculations, as I always allot 12% in my accounting, to be shaved of by the affiliate marketing networks that I use. But, ofcourse this does not mean that each time some earning is shaved off, you must not contact them for a clarification and possibily a return of the earnings back to you. In a few of the cases so far where earnings "shaving" happened, they investigatedand I got back what was deducted.