We're aware of this issue. It is rather embarrassing. Unfortunately, the fix is rather involved, so we don't have it ready yet. The issue is less likely to happen if you sync when you start and finish using OmniFocus on each device. (The iOS apps automatically start a sync as you switch away from them.)
We do have a 30-day guarantee, so if you'd like a refund, you can call or email
sales@omnigroup.com
We try to keep up with these forums, but for a more timely response, please email
omnifocus@omnigroup.com or call 1 (800) 315-6664 or 1 (206) 523-4152.