It sounds like there is some issue with the Run Command extension the VM. You can try rebooting the VM to see if that resolves the issue.
If you are still facing the same issue, please try uninstalling run command and rerunning, this will resolve most of the common issues. Known issues with the extension can be found here.
Hope this helps. If you are still facing issues please include information from the log file typically located in the following directory: C:\WindowsAzure\Logs\Plugins\Microsoft.CPlat.Core.RunCommandWindows\<version>\RunCommandExtension.log
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