I think I understand what you're asking, and what you're seeing, and yes, it does have to do with the breadcrumbs.
Right now, my breadcrumbs show "The Rocketry Forum > General Discussions > The Watering Hole > Why do forum index links disappear from time to time?"
If I click on "General Discussions" I will only see the forums in that category. If I click on "The Rocketry Forum" then I will see all categories, and all forums in those categories.
I suspect (but could be wrong) that you're clicking on a category, and only seeing the forums there, when that's not the behavior you necessarily expected.
-Kevin