I literally just started today. I played a little and then got Freelancer Companion, I changed the directory in which Freelancer was in, restarted both programs and came back to find myself insta-banned?
It's probably not related to Freelancer Companion - I haven't heard of any other players getting banned after installing or playing with it open, at least.
The administration team will need some character names to check what's happened (and for unbanning you), so I'd suggest following the official guidelines for cases like this and making a post in this thread with one or more of the character names on the account that is banned, and explaining what's happened.