I had 2 Sanctuary of Saerielle badges for completing quests. then I participated in one of the events and earned another. the 1 badge stacked separate from the other badges. None of the badges ever showed up in the Current City Badges. DO you know why this is happening, and/or how to fix it?

The badges won't show up in Current City Badges until you use them. You have to click on them in your inventory and click 'use item', then it will show up ^.^ As for them not stacking, you can probably stack them manually, but since you're just going to use them anyway, probably not a big issue.