If you don't have 'showdead' turned on in your profile, what could be happening is that those articles are so heavily flagged that they're almost all [dead], in which case only users with that setting turned on would see them.

Articles that show [flagged] but are not [dead] have actually been flagged less (relative to upvotes) than articles which get flagkilled, i.e. flagged all the way to the [dead] state, where they cease to be visible to most users.

(Here are a bunch of past explanations about 'showdead' in case anyone wants more: https://hn.algolia.com/?dateRange=all&page=0&prefix=false&qu...)