Yeah, thanks for the report. First of all I want to tell why I have changed the way of minimize.
The system that was on v.6.3 worked actually good until the point where sometimes LJTD was not anymore on the top of the game and just a restart of LJTD was a solution. The reason was that the minimizing routine lead to this misbehaviour. I did some changes and got it working on 2 Test Systems (Win 8.1 and Win 7).
Do you have the latest .Net Framework installed? Could you upload your config file? So I can have a look there, too.