I has a similar issue that i initially blamed on app stacks.
Symptoms:
After logging in as a user, I would see the "Welcome" screen for minutes to hours
AppStacks (writable volumes and apps) would attach
I wouldn't see the user as connected in the connection server admin web console
I would need to remove the desktop before the app stack would show as unattached.
The issue came down to bad DNS records in AD.
Set DNS to allow secure and non-secure updates
Set Scavenging to 4-8 hours
Set DHCP lease time to 4 hours
Setup a post sync script on the base image that runs ipconfig /registerdns
ideally you want your DNS records to be as close to "real time" as possible for non-persistent desktops.