Even if ignored, all the rares still pop up in Zaralek Cavern.

What character you do the ignoring on does not matter.
It works in other zones regardless of which character you are on when you click the checkbox. This issue is zone specific.

Yep. And in my case,

I ignored those on the same profile but using a different character.

They only show in the list after they spawned, and they correctly show as ignored.
However they are actually not ignored...

Not sure if the fact that I ignored those on the same profile but with another char plays a role or not.

The fact that it works in a given situation doesn't guarantee that it doesn't play a role when it breaks.
I am just giving every details that I have in case some can help, albeit those might prove to be of no importance.
Maybe you have enough knowledge of the code and how it handles things to be sure, I do not have such knowledge.

Oh, from the screenshot, that one is specifically because you're only ignoring the vignettes -- it'll still notify you if you see them in other ways. If you want to ignore everything about the rare, you need to do it in the "mobs" section of the settings. (Shortcut is by right-clicking the close button on the popup.)

The design logic here is that ignoring vignettes is mostly for ignoring spammy treasures.

Oh, thanks, good to know! :)