I have the same problem with a Vans B727-200RE. I have an awesome panel for it, it is a great plane, but I cannot get the A/T to hold no matter what. I think there is something missing in the aircraft.cfg, but I have no idea how to edit this file to correct the problem. I don't think it is the panel config, because I have tried different panels with this plane, I have the same glitch no A/T. Also, I can't get this plane to work with FDC Livecockpit!!! that really sucks!!! I have set the flaps to match the plane as FDC will not connect if the flaps don't match, but i have matched the flaps and still no connection. I refuse to delete this plane I WILL get it to work I just need some advice on correcting these problems. If I get any info. on this issue I will be sure to post it here for you!
