The latest version of the Windows Azure PowerShell module v 0.7.0 (released 21-10-2013), which features such great improvements as Windows Azure Active Directory logon support, unfortunately has a bug relating to endpoint ACLs.
Any Set-AzureEndpoint or Add-AzureEndpoint command which includes the ACL parameter will seem to succeed, but no ACL changes will be applied to the endpoint. I reverted to the previous release, v 0.6.16.1, and it works correctly.
I submitted an issue on GitHub, hopefully it will be resolved soon.