This is the response I got from Southern when I made a complaint about Advance tickets always being rejected. It seems it is a conscious decision from GTR rather than poor gateline programming - maybe they've set the gates to reject them by removing all Advances from the database rather than using special rules.
It's a poor customer experience and you don't even get the revenue protection benefits, because when the gates are set to reject so many tickets the assistants just wave anyone through who has a bit of orange paper and/or looks honest.
When I've asked the assistants why they are rejected, many don't seem to know the official line, usually get an answer like "the machines are old" or "the machines are stupid".