Sorry for the trouble here, Stapleton! Based on the description, I'd expect them to be working. Maybe double-check that the "Alert Style:none" option hasn't accidentally been selected for OmniFocus in Settings.app?
If that isn't the issue, (and forgive me if you've already checked these, just being thorough) it may help to double-check that OmniFocus appears in the "In Notification Center" section.
If
that doesn't help, send our
support ninjas an email and we'll be happy to investigate what's going on here. Apologies again for the trouble!