I went from a personal account to an organization account. Do I have to uninstall my Pulumi app on github and re-install it? It seems like the permissions for the Organization are not registering.

You do need to establish a relationship between the Pulumi Org and github app. You may be able to do that from the github side, but the easiest approach is likely to just uninstall and reinstall from the Pulumi org’s settings page.