The most common reason why the amount of autopaid freelancer royalties a recipient received into the Affiliate Credits section of their customer account does not match the total on a freelancer royalty report, is due to the timing of when the autopay freelancer royalty was set-up.
Autopaid royalties are calculated, deducted from publisher earnings, and credited to the freelancer's customer account in real-time when a sale is made. If the publisher has not yet set-up the freelancer royalty when the sale is made, then the freelancer will get no credit on that sale.
Our database structure does not easily allow us to distinguish this when we query it to provide information in freelancer royalty reports. Therefore if you run the freelancer royalty report over a large span of time, the report assumes the current freelancer royalty rate was in place for every sale during that time period.
This is better explained in example. Here is a section of a Detailed Sales Report run under a publisher account:
From this report, you can see that the publisher account was credited a full, non-exclusive 65% earnings rate on the first two sales of the Stock Art.
Then subsequent sales only see a 32.5% rate for the publisher, because a 32.5% autopay freelancer royalty was set-up after the June 26th sale and directed half of the earnings to the freelancer.
If the publisher or freelancer ran a royalty report on March 7th, 2015 that covered this entire date range, the report would assume the 32.5% autopay freelancer royalty was in place for all of the sales. The report would therefore over-report earnings vs. the amount the freelancer was actually paid. The report would assume freelancer royalties were paid on the first two sales, even though the freelancer royalty was not paid because it had not been set-up yet by the publisher.
Publishers can verify which sales were paid or not by using their main sales report page to run a custom sales report using the "Show details of each individual sale" setting and see (as in the example above) which sales had the autopay royalty deducted and which did not. The publisher would need to send any missing royalties directly to the freelancer.