Hey, the exact same thing happened to me after rebuilding my carbs. I bench synced them, hooked them up, and put the carbtune on. I started the engine and noticed that not even my #2 carb (the base non-adjustable carb on older models) was pulling a vacuum reading. I thought maybe my carbtune was bad! How could my engine not be creating vacuum?? However, I went ahead and started adjusting the carb slides anyway, just to see if there would be a change on the gauges. And sure enough, one by one they started popping up on the carbtune. What I thought was a pretty close bench sync, was still WAY OFF. Hook your morgan back up, start the engine, and begin adjusting your slides. You'll soon notice the reading on those vacuum gauges starting to rise.
Good luck!