The Timeout is a warning and hence you are unable to catch it. Searching a little, I found a couple of references that might be helpful:
http://www.mathworks.com/matlabcentral/newsreader/view_thread/158768 http://blogs.mathworks.com/loren/2006/10/18/controlling-warning-messages-and-state/
May be something like this:
lastwarn('');
try
fread(s)
if(~isempty(lastwarn))
error(lastwarn)
end
catch err
err
end
