I am using version 1.2.11 of GitHub for windows. As shown in the screenshot below, the same repository is listed multiple times, and I don't know how to clean it up (note: names are censored, but colour coded: the black items are all the same, and the maroon items are all the same).
The github release notes indicate that a problem involving "Duplicate entries Git error for some repositories" was fixed as of 1.0.30, but I still encounter the below situation.
The other posts that I have come across include how to duplicate repositories in the GUI, but I haven't found an answer regarding how to remove the entries from the GitHub GUI for Windows. Note: on github.com there is only one instance of each repo, but in the GUI multiple entries are shown (they all link to the same repo) in various quantities. Also note: one of the "dungeons" entries (the purple one) is a fork of the other.
Image:
If you're running the latest version and it's supposed to have fixed the bug, the best thing you could do is to contact them and provide as much information as you can. They'll for sure reply soon asking for further information, and clearly telling you how to get it.
There's probably an issue left, and you can help them solve it - and it's always a pleasure to talk with GitHub's support guys :)