If you want to use UNC paths, configure Auto-import to use those, instead of Windows paths. That way, your playlists will just work.
Otherwise, you'll need to configure your playlist generation software to use Windows paths. You can use mapped drives and configure SBS or LMS to use those. This way, all your music is visible across the network as, for example, M:\Music. But this obviously won't work if your SBS/LMS server is running on a *nix box and you're using native paths (vs. samba paths).
If MC has both path formats, and auto-import wasn't configured to find the playlists, at some point you must have imported the playlists. You can remove the duplicate file entries in MC by simply using the Search box in Wizard mode (to make it easier for you) and query against the Filename (path) field, searching for files that start with your UNC path. Then you can select the results, and hit Delete to remove them from MC's database.