Duplicate folders

I have set up 4 root folders with different project names. In those folders I will have subfolders that will have my information in them. When I create a sub-folder in one of my root folders, a copy of it appears in another root-folder(just one and allways the same one) and if I try to delete either one, they both disappear. Any thoughts?

If your root folders point to the same physical path, this is the expected behaviour.
Please set separate paths for each root folder.