basically, either run the Rebuild Forum Information in Maintenance->Update counters.
What this calls is basically build_forum_permissions....which in turns calls build_forum_genealogy....which updates the genealogy of your forums (specifically the childlist and parentlist fields) which are necessary to show up in vB.
I have an external interface to add forums to my vB site. I also have a cron job that runs every hour to see if there's any new forums added. If so, it calls build_forum_permissions to update everything.
Hope this helps.
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