Settings are configured correctly but icons for treasures already looted aren't removed from the map. I tested with a different addon and it works as expected so it's a bug in this one, whose details I otherwise prefer.

For each of these chests there is a hidden quest that gets completed , similarly to killing rare mobs, when you loot them.
This might just mean that the addon is looking for the wrong id. To test this, it would be useful to show the exact location, hopefully with coordinates to be able to figure this out faster.

Can do. When I'm next questing there, I'll pick one and collect its details and take screenshots, as well as of the handynote settings.

I took a character to Val'sharah and opened one, and the one I chose worked correctly. Of course, I may have the wrong questID for only some of them -- could you point out specific coordinates for a chest that isn't hiding for you?

Aaaaaaactually, I just paid closer attention to your screenshot, and it says that you've completed the associated quest. Could you double-check and confirm that you don't have "show found" turned on?

(If it's on, you might have accidentally triggered it -- you can alt-click the map button as a shortcut to do so.)