run script from desktop shortcut vs command window

I set up a shortcut icon on my desktop to execute the following -

C:\Program Files\MATLAB\R2016a\bin\matlab.exe" -nodesktop -nosplash -minimize -r matlabserial

Matlabserial.m opens a serial com port and reads NMEA data from a GPS receiver.

When I launch the shortcut everything opens and the script runs to the point where I look for data on the serial port. The script then times out with no data received.

If I type matlabserial in the Matlab command window the script executes without a problem.

I put a disp('looking') command right before the lines

    data1 = fgetl(obj1); % GGA
    data2 = fgetl(obj1); % ATT

when launched from the shortcut I get one response. When launched from the command window a response for every time it finds the lines of data on the serial port.

I checked the path and all my subdirectories and toolkits showup.

Is the desktop shortcut not allowing the serial ports to work?