Make sure to get the data sheets for the shields and read over them. I was having all kinds of similiar problems with my sabertooth 2x25 going off the included "quick start" guide for analog mode. When I downloaded the entire manual from the site, I found some very pertinent info that was causing my problem. Basically, in analog mode and controlled by a microcontroller, I had to make a separate circuit in between the digital signal out and the H-Bridge, or else the 2 signals interfered with each other.