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Hi there,
Indeed at a first glance, this does not really make sense. This could be explained if the server configuration is different, for example, if setup B is better tweaked in terms of PHP and MySQL settings and etc.
What I could suggest in this case is to do the following:
Add some logging in your application to verify that the two environments are actually processing the same data. As if there is a lot less data to be processed on one of the systems it would explain why it is faster.
Monitor the resource utilization on the two environments to verify that the resources are actually fully utilized and not sitting idle.
Check the error logs to make sure that there are no errors that could be causing the delay.
Let me know how it goes. Regards, Bobby