The parallel pool workers are separate MATLAB processes, so you might well need to create new serial port objects on the workers. I'm not too familiar with the serial port object in MATLAB, but it sounds like you can't have multiple objects referring to the same underlying port, so you probably need to ensure you only build the object on one worker, something like this:
% build the serial port object
spmd
if labindex == 1
s = serial('COM1');
else
s = [];
end
end
% Use the serial port object on lab 1
spmd
if labindex == 1
f1(s);
else
f2();
end
end
