The other day I combined 2 of my Google Apps domains by adding the second as a domain alias. The problem was that the alias appeared to be stuck and the only option would be “Activate domain alias”. I had already activated the alias by 2 methods so I had no idea what was wrong.
I then read on the forums that being signed in to multiple accounts could prevent a successful activation. I immediately signed off all my accounts and retried. This time, I got an error, saying that Google Webmaster Tools is not enabled for my domain. After activating that service I managed to finally activate the alias.
The root cause of the fail would be something in the lines of: Google detects that you don’t have access to the Google Webmaster Tools and switches to one of the other accounts you may be signed in. That account’s GWT service might be activate, but it doesn’t have permission to deal with your initial domain hence the errorless loop of trying to activate the alias.
Activating a domain alias is a pretty simple process but if you never get an error it is hard to figure out what could be the problem.