The EC2 AMI updates for WebPageTest include this commit. Prior to that test agents weren’t able to communicate with WPT servers that required HTTPS.
In case you ran into this here is the simple work around. Let the test agent connect to WPT once ( via plain HTTP ), it will look for updates ( and install them ), then switch to HTTPS. If that isn’t an option you can download just the Windows test agent code and update it manually ( not nearly as fun as the automatic update process ).