COM3 operation requires some configuration before it will function properly. If you refer to page 134 in the OEMV installation & Operation Manual http://www.novatel.com/Documents/Manuals/om-20000093.pdf , you will see that COM3_Rx and COM3_Tx are multiplexed with USB D (+) and Event1 respectively.
You need to first disable Event1 by using the MARKCONTROL command then enable COM3 by issuing the INTERFACEMODE command.
The correct sequence is illustrated below:
(To disable Event1) MARKCONTROL MARK1 DISABLE (Enable COM3)
INTERFACEMODE COM3 NOVATEL NOVATEL
NOTE: DO NOT connect a USB cable while using COM3 (reference page 137 OEMV installation manual)