Apple asked us to switch to their public API for approving untrusted certificates in 1.6.1. The warning you're seeing is a normal part of the API, and once you select "Trust always", shouldn't ask you to approve again (unless you turn off Bonjour sync, then turn it back on, since you're effectively generating a new self-signed certificate). Hope this clears things up!
Sefbro, it sounds like something else may be going on in your case; if you email
omnifocus@omnigroup.com, or call us at 800.315.6664, we can help. Thanks!