When I try to communicate with a serial device, I get an error.

I see my serial device in the MATLAB instrument control app. And it appears I am able to connect to it. However, when I try to communicate with the device (using commands that work when I connect the device through PuTTY), I either get "A timeout occurred before the terminator was reached" when I query, or "An error occurred while communicating with the instrument" when I write. Any help would be greatly appreciated.