I meant to reply earlier and got sidetracked, sorry. What you may need to do, and it will be tedious since you have so many things, is look at each "wrong" item and see what could be causing it. Sometimes, if there is one word that is duplicated in the title it will pull it through. Do you see what I mean? You may have to mess with it for a bit. I would choose a category that you have the fewest items in that you are having this issue with, and go through it to check the wordings and see what could be throwing it off. I usually have multiple windows open so I can just switch back and forth as I make the updates in the categories. That way you can just refresh the page with the store on to see if the changes "take".
Also, I've noticed that sometimes you have to refresh the page with your store a couple time to have the changes show. I don't know why, but it does that sometimes. Just a quirk I guess. Once you do one category, I have a feeling you'll get the hang of it and figure out what you need to do to get all the categories to show right.
I'm new, as I said before, but I'd be happy to help you out some more if you'd like. I know it is really frustrating learning this system, but it really is great once you figure it all out.
