I had problems like that as well (last nights was the first chance I've had to use the new mount). I think I worked it out in my sleep last night though. Spent the whole damn night dreaming about cables and mounts. It was like a nest of snakes. Which is how I managed to work out what I was doing wrong.
I hadn't connected a serial cable from the laptop to the StarMate to actually carry any information for the mount to make adjustments.

And that was after sending an email to Robby asking how to do it.
Straight down to Dick Smiths this morning to pick up a serial cable

And a usb extension and a usb multihub (only one port on the Laptop)
I hope Robby chimes in. That will save me another night of experimenting.