Assume the following "Shell Script":

#!/usr/local/bin/php -q
<?php
  print("blafasel.\n");
?>

With the Zend Optimizer switched on the script's output is:

[markus@testmoehre]$ ./test.php
#!/usr/local/bin/php -q
blafasel.
[markus@testmoehre]$

Notice the first line, which shouldn't be there.
After removing (or commenting) the lines

  zend_optimizer.optimization_level=15
  zend_extension="/usr/local/lib/zend/ZendOptimizer.so"

in php.ini, the output is as expected (i.e. without the first line).