There's a few different causes of this. I don't know of a single solution that will fix it for everyone. You're best off emailing or calling a Support Ninja, so that they can coach you through the troubleshooting steps.
800 315-6664 or +1 206-523-4152 or
omnifocus@omnigroup.com
(We're also working on an update to the app which will fix a few of these situations.)