My first thought would be to increase travel speed and WFS toward the top of your range, as well as inductence to closer to maximum. Assuming that your GMA welds are done at top dead center, 1G with rotated pipe, on your new setup.
If the tacks are feathered out, a good hot root pass should provide full penn on the back and a flat to slightly concave face, while melting into your tacks with no lack of fusion. With the added control and consistancy (assuming good fit-ups) of your new system, you should be able to go much hotter and faster than when you were doing the joints manually.
Tell us more about your parameters and fitup...
Voltage
Wire feed speed
Root opening
Root face
Travel Speed
Postion of weld