Sometimes your web application requires a forms based authentication provider. After you implement the new provider and disable Windows Authentication, some of your PowerShell functionality will stop working when you use for instance the farm account. This is normal, because your web application is unaware of any Windows Authentication provider.
A “solution” is to add the account, which you wish to use with PowerShell, as a “Full Control” user to the Web Application User Policy:
After adding the account, PowerShell will get its full functionality again because your credentials are recognized.
When you check on your IIS level, you’ll notice that Windows Authentication will be enabled:
But, because there’s no Windows Authentication Provider configured on SharePoint, you won’t be able to login directly to your sites using a windows account.
This way of working is an alternative to the web application extend method; Which provides a lot of other usages for authentication mechanisms, but aren’t always needed, like in this example.