What I've seen of Tony this year, he doesn't look like he's using the ability to play. It looks to me like it's certain types of passes he's sailing (mostly throws to the flat or crossing routes to his left), and then he's pretty clearly hesitant to throw to two of his WRs, which adds an additional burden to his split-second decision making process. It's making him less effective.
I'd guess his physical problem is probably either mechanical, or he's got a nagging muscle issue of some sort that affects his mechanics in certain situations. And I suspect the later, but I don't know enough about QB mechanics to say what it might be.
When asked whether Jason Garrett is the right head coach for this team: "I don't think there is anyone else that could. I think he is an unbelievable coach. We've responded to him and he has made us better football players, better people. If you watch us I think we play with a certain relentless spirit." --Sean Lee