Ok, I finally got it working by changing the serial port settings prior to running it

stty -F /dev/ttyS1 raw speed 115200

For some reason when my system boots up it has the serial port set to 9600 baud and to strip the 8th bit from each character (istrip option). I had kind of assumed emptool and upgclient would set the proper port settings for me like I've seen other programs do, but I guess they don't.