When using msdeploy and the msdeploy.axd handler any attempts to deploy to my remote server is met with a 401 not authorized error and the server logs
IIS
This might depend on how you're specifying the connection on the client side as well - if you're using msdeploy.exe you would specify the computername argument including a "?site=" query so that you connect at that site level rather than the server level, for example:
msdeploy.exe -verb:dump -source:iisapp="siteName",computername=https://servername:8172/msdeploy.axd?site=siteName,username=user,password=pass,authType=basic [-allowUntrusted]