I turned filter off, option is unchecked, but it doesn't change anything. Achievements still appear on the mini list, more than that - even if I have said achievement already done.

...addon also started to show "Titanforged" group on minilist, but that's another issue, I guess.

That's because achievements are used as headers. You will still see them but they will count as --- not affecting numbers and if they contain 0 items then they won't show up at all.