While I'm not saying that this could not possibly happen due to some so-far unknown vulnerability, there are more likely possibilities that are worth...
If the command works from the command line (when you are logged in as the user whose cron will run the task) then it will run in cron. Otherwise you...
It sounds as though you have a lot of different things going on, and potentially that you have some .htaccess mod_rewrite rules going on that may be...
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