Unable to use SAM-ICE with Sam-ba

I am trying to use the SAM-ICE with Sam-ba to program my AT91SAM3U-EK. Initially I didn’t have any problem getting Sam-ba to run on the PC side. When you start Sam-ba it asks for the communications interface and the board. I can select /jlink/ARM0 and the board but when I press connect I get the message “No valid processor ID found.” I don’t have any problem programming the board using the /usb/ARM0 interface and my code executes as it should. I can also talk to the chip using GDB and the J-Link software doesn’t have any problem reading the processor ID. Does anyone know of any solutions?