Yet another question / issue.
I missed to trigger that quest before going to Nalisa Shrine. I got the orb and then realized what I had missed, so I went back and triggered it. I passed the orb over and did get a quest complete and a quest bonus.
However, the quest still appears in white in the journal and so does the first line of the quest description ("Check out a nearby shrine"). There seems to be no way to get rid of this now.
It's not really a problem since the quest has been counted, but it's a little bit disturbing.