Does your Search Articles page show a category called "Category" lumped in with your real categories? Do you have a "SubCategory" too??
These were set up during the development process to populate your category lists. Now that you have real data on your site, you can get rid of these generic category labels.
Just go to your Site Variables listing for your site and find the one for Articles Category. Change the default name from "Category" to a basic category you currently use on your site, such as "Member News" or "Community Events". Do the same for Articles Subcategory.
Use this same process to get rid of the generic categories in Directories.
Not sure how to change your site variables? Contact Schipul at 281.497.6567 and anyone here can walk you through it!