[heftig]

Looking into why this is persistent, I discovered it's stored in Minion's config.xml.

The cause of this problem is addons getting designated as children of other addons, e.g. the Auctioneer suite was designated a child of the BeanCounter addon for me:

<AddOn name="BeanCounter">
  <UID>7879</UID>
  <Children>
    <Child>Auc-Advanced</Child>
    <Child>Auc-Filter-Basic</Child>
    <Child>Auc-ScanData</Child>
    <Child>Auc-Stat-Histogram</Child>
    <Child>Auc-Stat-iLevel</Child>
    <Child>Auc-Stat-Purchased</Child>
    <Child>Auc-Stat-Simple</Child>
    <Child>Auc-Stat-StdDev</Child>
    <Child>Auc-Util-FixAH</Child>
    <Child>Enchantrix</Child>
    <Child>Enchantrix-Barker</Child>
    <Child>Informant</Child>
    <Child>SlideBar</Child>
    <Child>!Swatter</Child>
  </Children>
</AddOn>

These child addons aren't displayed. Rather, they're handled together with their parent addon. Or that's what I assume, anyway.

Looking further, it seems the Auctioneer addons are children of each other. Is this supposed to happen?