When you deploy multiple instances to VM Role along with Windows Azure Connect and domain join setting , it may possible that domain join may work in one VM instance but not in others. I happen to worked on such issue and here are the details:

 

You must collect the diagnostics log in virtual machine where problem occurred along with other machine where it doesn't. To collect diagnostics log in Windows Azure Connect:

http://blogs.msdn.com/b/avkashchauhan/archive/2011/05/17/collecting-diagnostics-information-for-windows-azure-connect-related-issues.aspx

 

Investigation:

After our investigation we found that both instances had same original machine name, when they should have random machine names from running sysprep /generalize before uploading. It is possible that you may have missed the “Generalize” checkbox setting during “Sysprep” your VHD.

Solution:

  • Please change the VM Role instances names to unique machine name
  • Reboot your Virtual Machine
  • Try Windows Azure connect with Domain Join and it will work

To avoid the above problem all together, please don't forget the check "Generalize" option during Sysprep step as below: