Duplicate of all my pictures after reinstalling everything

My macbook was getting full of junk and has been running slow so I decided to reinstall everything with the system restore disks...It all worked great, I backed everything up and all that. I put everything back on my macbook and then went to look at some of my pictures the other day and realized that there are duplicates and some of the folders there is even 3 and four copy's. When you open the folder some of the pictures are good and others are horrible quality...what did I do wrong and how do I fix it? I need to know since I just ordered a bigger hard drive and I'm going to be doing this all again in a day or so...