Did some updates on the site and all my categories un-sorted. I tried deleting all of them and importing the sorted csv file and either only a few products show or none show. If I import the file to a new shop I get all of them sorted. I was able to build the site off of importing, and that's how I update, but for some reason now it only does it on a new site. Any suggestions?

Save your site under a new name then try clearing out all the products then import your csv.