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I've seen it happen once or twice that the attachments don't seem to show up until I quit and restart OmniFocus. After that it works as expected. You might look to see if there are any messages from OmniFocus in your Console log regarding attachments. In my case, it looked like the library that unpacks zip files got terminally confused somehow.

If restarting doesn't do the trick, contact Omni support at or 800-315-OMNI or +1-206-523-4152 and they'll investigate with you.