That's crazy we had the same issue with 2 clients this week. I think Amazon and Kentico aren't playing nice somehow. The two things we have come up with at BizStream are 1) Contact Amazon and ask them to remove the throttle and 2) Try adding multiple SMTP servers (clones with the same SES info) into the Kentico SMTP server bank (EMS license required). We are hoping that by having multiple connections round robin through to SES helps.
We are still testing to find out the results if either or both tactics above help.
Post back here if you have other ideas or if one of these tactics work for you.