Whenever you mess up with authentication methods on the IIS or through powershell, services may not function properly, especially the published ones. Blew is the default authentication methods published at Exchange Team Blog site:
Exchange Server 2010 with the Client Access Server (standalone):
Location
Authentication
SSL Setting
Management
Default Web Site
Anonymous
Required
IIS Management Console
aspnet_client
Autodiscover
Anonymous / Basic / Windows Authentication
Exchange Management Shell
ECP
Anonymous / Basic
Exchange Management Console or Shell
EWS
Anonymous / Windows Authentication
Microsoft-Server-ActiveSync
Basic
OWA
Powershell
Not Required
RPC
Basic / Windows Authentication
RpcWithCert
all options Disabled
Required (128 bit not checked)
N/A
OAB
Windows Authentication
Exchange Server 2010 Mailbox role (standalone):
PowerShell
CMDlet list for those that can only be modified in the Management Shell:
Set-AutoDiscoverVirtualDirectory
Set-WebServicesVirtualDirectory
Set-PowershellVirtualDirectory
Set-OutlookAnywhere (for the RPC virtual directory)