If you configure delegation to "Allow administrators to bypass rules" and msdeploy command succeeds, then you are going through WMSvc and it is letting you through. Otherwise, from the response it seems that WMSvc is rejecting you and you are falling back to Web Deloy agent.
Set/add the following reg value to WMSvc reg key:
reg add HKLMSoftwareMicrosoftWebManagementServer /v WindowsAuthenticationEnabled /t REG_DWORD /d 1
Recycle WMSvc:
net stop wmsvc & net start wmsvc
Try again. If it doesn't succeed, can you post your msdeploy command line.
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