Sometimes you have spurious entries that cannot be removed from the UI.
You can manually edit the Repository Registry by going to the local configuration directory--something like: C:\Users\username\AppData\Roaming\TortoiseHg--and editing the file:
thg-reporegistry.xml
If you have an empty group, there will be a line like:
<allgroup name="default"/>
which you can just delete.
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