Is the script identical, are you submitting exactly the same parameters? I find that data is what really makes the PHP footprint grow, a big associative array or a large set of models and memory usage explodes.
I am wondering if you are turning xdebug on and off, xdebug adds a huge amount of overhead to script execution also.
If it’s nothing obvious, you might have to ask somewhere where they are more expert on PHP internals.