Since installing the most recent version items that have been collected are not showing up as such.

Hmmm did you try Shift-Clicking the Minimap button or an ATT window? Sometimes the Server doesn't properly send the game Client the event to indicate that you've learned a new appearance, so ATT doesn't detect it. By performing a 'force' refresh, you cause ATT to go check all the appearances (among other things) to verify everything is synced up.

@Smeghead113 Any changes to this since you've posted or has it been fixed in the latest version 2.4.9?

Gonna assume this is a fluke or otherwise resolved :)