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It's not clear from the code here whether or not you used a specific php.ini that loads phalcon.so for the non-phalcon benchmarks. Loading a blank page with phalcon.so has a non-trivial overhead over a blank page without phalcon.so being loaded. As such, the non-phalcon benchmarks should all make sure that phalcon is not being loaded when they're run.
You may have done this but it's not clear.
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