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Sorry for the confusion! If you open OmniFocus' preferences and switch to the iCal tab, do the "missing" contexts appear in the "Unsynchronized" category?
(Select that entry in the list on the left of the pane: your contexts will appear in the pane on the right.)

If so, select the contexts you want to synchronize and drag them to one of the other entries in the calendar list.

If the missing items do not appear in the Unsynchronized section, is the "Add blocked actions to calendars" box checked? If not, checking that box may resolve this.

Hope this helps, but if you still aren't seeing what you expect, email our support ninjas and we'll be happy to investigate this with you.