DG,
Sorry the delay in responding.
GEP never supported any type of authentication other than username/password to retrieve tokens in 10.2. Going through WebAdaptor was not supported at 10.2.
For 10.2.1, you should register a connection entering the URL that allows GEP to ask your ArcGIS Server what it uses to generate tokens. So if your WebAdaptor doesn't allow requests to generate tokens, then you can't use that URL.
During registration, after entering the URL set "Do you with to use token?" to "Yes" and enter the URL to your ArcGIS Server. If it's the correct URL, you'll see a section pop up telling you where to get a token from. Do you see this?
-Javier