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configuration - Cannot turn off short_open_tag with ini_set

I'm embedding a javascript syntax highlighter to a PHP script that reads source file and echos it back. The js highlighter has this string on one line:

... [z,/^[^<?]+/], ...

The short_open_tag is on on this server and the <? in the string confuses the script and causes errors. I cannot turn off in php.ini or elsewhere.

I have used ini_set('short_open_tag', '0'); in the same script, but it does not take effect. What could be the problem?

Edit

In the end, I used what Col Shrapnel suggested in a comment:
I changed [z,/^[^<?]+/], to [z,/^[^<?php echo '<' .'?'; ?>]+/],

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'short_open_tag' is marked as PHP_INI_PERDIR in PHP <5.3.0, which means you can't change it with ini_set().


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