Problem with permalinks & url shortner

I am using the url shortner plugin and as a result of something I have done, it works for some pages fine and for some pages it generates a link back to my main default site that I use for the template to create all my sites.

If I edit the page, the permalink displayed is in fact correct and I have never edited that.

However, if I just click the edit button (DON'T CHANGE ANYTHING) then click ok and save the page, my link shortener now generates all the correct links.

So now I need to figure out how to do that for all of my pages on all sites?

Any idea what info is being changed in the database and in which table when I resave that permalink?