I have an MVC 4 website using a WCF service. When I deploy to Windows Azure using the VS 2012 publish wizard, I get this error:
10:13:19 AM - The HTTP request to 'https://management.core.windows.net/42d4257b-5f38-400d-aac5-2e7acee9597d/services/hostedservices/myapp?embed-detail=true' has exceeded the allotted timeout of 00:01:00. The time allotted to this operation may have been a portion of a longer timeout.
After cleaning the project and publishing a few times, the error goes away. What am I doing wrong?
Whenever you start publish process from VS machine, a SSL tunnel is established first and once the tunnel is created, the package is transferred from your machine to Windows Azure Portal first. After the upload is completed, you will see the result notifications are posted back to Publish result windows and that is how it happens.
In your case, the time to build the SSL tunnel doe secure package transfer is longer then normal, this could be because of network latency between your machine and the Windows Azure Management Portal. For security reason the time to create the tunnel smaller windows and if the connection is not created, the retry cycle starts the process again and even if that fails you are greeted with the failure message. This could be caused by excessive traffic on either side or both sides. So this is mainly a networking related issue rather then specific to Windows Azure as after some time successive tries, you could upload your package.
In such failure/situation, you can run network capture utilities i.e netmon, wireshark, and see the time taken during failure and success to see the different in various transfer. This will help you to understand the underlying delaying issues.
Try to update your roles diagnostics like below

then update your storage credentials because it may be expired.

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