I searched for the answer on the net for hours yesterday. The question has been up on stackoverflow a number of times, and it seems the answer is that it isn't possible in Window: You cannot run Matlab silent in Windows! Sounds crazy (or maybe like a bug). I have rewritten my script, so now it always runs and waits for a file to exists. This file is created by my Perl script at the point where I had the system call for Matlab. Sigh.
If it is possible to run Matlab silent in Windows, please tell me how. I would still like to know.