You should only get duplicates like this if there are multiple copies of a file, or multiple paths to the same file.
In a File list, add a Filename (path) column, and compare the paths of what appears to be duplicate files. If you see that the duplication is due to importing the same set of files via two different paths (eg. a windows drive path vs. a UNC path), you can sort by Filename (path) and remove the redundant items. And remove the extraneous auto-import entry (Tools > Import > Configure Auto-Import...).