First, please read Writeup Formatting Tips, since your lack of <code> tags seriously impedes the legibility of your post. As well, the liberal addition of some <p> tags to break up the text would be helpful.

I can say there are no immediately clear errors in the posted code, but again I have not worked with MATLAB on the command line for quite some time. You do some things I would consider quite poor form, such as not testing for the success of your open, using bareword file handles and using 2-argument open, but these are not syntax errors.

A potentially much cleaner solution is rather than piping into the executable is use your Perl script to explicitly generate a .m file, and then execute the .m using system or backticks. In this way, you will have an audit trail so you can figure out which language is giving you problems - I frequently take this autogeneration approach with auxilliary programs. Remember that Perl was originally designed for text processing and does it exceptionally well. Perhaps this will give you some ideas:

#!/usr/bin/perl
use strict;
use warnings;

open(my $matlab, '>', 'm_file.m');
print $matlab <<EOF;
x=1;
save timer;
EOF
system('matlab -nojvm -r m_file');
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