This sounds interesting.
First thing to check with the tabs is that you've included the main parent category along with the forums you want to use. So as an example let's say you have the forums below (a - indicating a sub level and the numbers reflecting the ID of the forums):
Category 1
- Forum 5
- Forum 6
-- Subforum 11
-- Subforum 12
- Forum 7
Category 2
- Forum 8
-- Subforum 13
-- Subforum 14
Category 3
- Forum 9
Category 4
- Forum 10
To make Forum 10 and Subforum 14 appear, you'd need to have Category 2, Forum 8, Subforum 14, Category 14 and Forum 10 selected. Usually forums not appearing is related to not including the parent forums and categories.
Regarding the pages requiring a hard refresh to appear, it might be you need to disable this setting:
AJAX Tabs Quick Load
That setting is designed to speed up the AJAX page load by only loading forum data. But some other plugins and mods require hooks that don't exist in that quick method. Disabling it might help fix that.
If those don't work, feel free to PM me some login information and I'll take a look at your setup. You can do that here or to my username
Mokonzi on the
http://www.dragonbyte-tech.com forums.
Hope this helps.
Matt