After adding HTTPS endpoint I get this warning: 'Microsoft.WindowsAzure.Plugins.PasswordEncryption' was not found in the certificate store

The WebRole is adding the RemoteAccess certificate settings and looking for the certificate in LocalMachine because SDK 1.8 adds <Import moduleName="RemoteAccess" /> to csdef file. To resolve this issue:

• Delete all "Microsoft.WindowsAzure.Plugins.RemoteAccess.* " in both (local & cloud) .cscfg files
• Delete "Certificate name="Microsoft.WindowsAzure.Plugins.RemoteAccess.PasswordEncryption" in both .cscfg files
• Delete <Import moduleName="RemoteAccess" /> and <Import moduleName="RemoteForwarder" /> from the csdef file.
• Save & recompile. If you need to activate the Remote Desktop later, then process is described in this article.

Or, you could just add the RDP cert to LocalMachine store.