When trying to view a site I have created through Helm I get Windows authentication pop-up prompts.
Have you got ColdFusion installed on the server? If so, make sure that wildcard mappings are not present on your domains. You can check this as follows:
1.) Open IIS
2.) Find the domain you are getting authentication prompts at.
3.) Right-click it and choose Properties.
4.) Choose the Home Directory tab.
5.) Click the Configuration button.
At the bottom - are there any application maps there? If this is the case, you have two choices:
a) Remove the mappings (it would be best to remove them from the Master IIS site and filter the changes down to all domains).
b) Give the HELMWEBUSERS group the appropriate permissions, as per the ColdFusion documentation.
Once this has been done, the authentication prompts should stop appearing.