Invalid max_execution_time showing within WordPress plugins

I am running a site on WordPress v4.01 . I have setup this site on my vps.
Recently I am noticing strange issue on its php.ini info that it shows up max_execution_time = 0 in most of every plugin that shows server side information. Rest of other php information’s are showing correct except max_execution But if I drop a phpinfo.php file for checking up my site php configuration for this wordpress installation dir then I am seeing max_execution has been given 120. This tools that I have used so far for look up : ithemes security , ServerBuddy.

Need to mention that my site using php 5.6 with fastcgi+apcu. Also I have another php 5.4 installed from OS. I tried to switch back to it and if i do then it shows max_execution that has been set for 5.4 php.ini (120). But if I set it to 5.6 for that site then it shows 0.

You might be thinking that 5.6 php.ini might have set max_execution = 0. But no.. it has been set as 120. Because I set that php 5.6 version for another site also where I noticed that it is showing correct execution for that site which has been set in php.ini 5.6.

Restarting server didn’t even helped also. Now I am not understanding what else could be overwriting this max_execution process?.

This is inside of site. where it shows wrong information: https://i.imgur.com/Bj0tv35.png

And this is phpinfo.php for that site dir: https://goo.gl/tWeF0P

Os Debian wheezy 64 bit.
Apache 2.2
Php 5.4 (default)+Fastcgi +Xcache, Php 5.6+Fastcgi+apcu

Any helpful advice would be great to resolve this.

Thanks.