Hi Carrie and welcome to the Tiki community!
(there are some other researchers in it )
Well, ensure that you have and understood the difference between "Global permissions", "Category (of content/objects) permissions" and "Object permissions": See Permissions
After that, make clear if you are using forums (that's what you say in your first paragraph) or articles (feature CMS in tiki), and what's the context of your question. I guess it's articles (cms) and not forums, for what you say afterwards.
Ok, said that, I've never used permissions on article topics, but as far as I remember , they had to be set (in previosu tiki releases) after you had created an article topic, you had to go there and edit that article topic, in order to see the icon of the key, which would allow you to set permissions on that specific article topic.
Ok, and if that doesn't work, it might be worth filling a bug report at http://dev.tiki.org
(it might very well be that article topic permissions have still some permission bug that needs to be squashed, so that your report, if needed, will be very helpful for developers willing to fix it: there are two at least willing to do so, as stated in the tikiwiki-devel list a few days ago)
Keep in mind that you can alternatively use category permissions, and these are much more tested, and should work like a charm. (they do for most of us, for many months already). Keep in mind that you can use categories in articles...
Hope this helps, and again: welcome to the Tiki community!