In 4.3 and under the first time you tried to do a team based action, such as refresh provisioning profiles, it would ask you to log in. It no longer does this in 4.4, it just assumes a team and refreshes… how do I teach Xcode there are multiple teams? It lists them under the teams in side bar of the organizer, but won’t let me refresh their profiles, or select them when creating new profiles.
To clarify, each team is under a different developer ID, and I can’t find any way to log in to different developer IDs to refresh the provisioning profiles. I can still log in to different ID’s when submitting apps to the app store, however this doesn’t seem to affect the provisioning profile refresh login ID.
Seems to be fixed in Xcode 4.4.1 (released yesterday, 7th August 2012).
And as Ivan stated correctly: It seems that all profiles from all teams are synced as long as you have the same apple id across all teams.
(Tested this by removing all profiles from Xcode in the Organizer and hit “Refresh”)
Update:
If you have different apple ids across multiple teams and the login dialog is still missing, you might have saved your credentials in your keychain. See comments #2 and #3 of this answer for a workaround.