Have not seen it before but a couple things you can try.

1.  If you right-click in your repository area, are you scanning for network repositories?  If you are, try unchecking it, then right-clicking are removing your two repositories, then re-enable the scan.  See if it only grabs one.

2.  Remove the existing repositories, uncheck the scan option and then manually add back just the one repository.

3.  Check your registry for duplicate entries.  Current User\Software\Laserfiche\Profile\IPdatabase.  See if you have multiple key in there.