Old repositories have finally disappeared for me as well, but only once
I removed this package: app-install-data-medibuntu. That package is a
recommended part of adding the Medibuntu repository, according to
https://help.ubuntu.com/community/Medibuntu#Adding%20the%20Repository .
Removing it seems to have made no noticeable difference other than
fixing this bug. I’m not sure if the bug is caused by the package or
merely exposed by it. Nathan, did you remove that package as well?
Anyway, I hope this helps track down the issue.

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Software-Center don't remove unactivated ppa's
https://bugs.launchpad.net/bugs/574155
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