[Brian]

If I remember correctly, one thing that could cause that error message was OmniFocus taking longer to start up (maybe due to syncing) than the AppleScript system was willing to wait for the clipping script to finish.

If that's not the cause, you'll probably want to email the Support Ninjas directly; we all browse the forums as we're able, but if you mail them, you're guaranteed a response.

It would probably help them if you launched Console.app (in your utilities folder) and entered "OmniFocus" into the search field in the toolbar. Copy-paste any info that appears in the window at this point into your mail to them, then repeat the process with "Mail". They may be able to tell what's going on by examining that info.