Strange apache behaviour when lauching an external binary called by a perl script

[ledoc@xxxxxxxxxxxxxxx]

Hello list,
I am currently setting up a web service running on CentOS 6.4. This service uses perl scripts (cgi-bin) launching an external homemade fortran compiled binary.
This last is triggered through a web form when the user ask for it. It is not a system service but an 'on demand' execution.

Here is the issue: when I boot my server, everything goes well except that this binary crashes systematically (with a kernel segfault) when called by my perl scripts.
If I restart manually the httpd service at the command line (service httpd restart) the issue is totally fixed. I examined apache/system logs and nothing suspicious can be found.

It appears that the problem occurs only when httpd is launched by /etc/rc[0-6].d startup directives. I tried to change the launch order of http (S85httpd by default) to any other position without success.
Even with a httpd restart scheduled several minutes after the last rc script by the 'at' command, the issue is still there.

To summarize, my web service is only functional (with no external binary crash) when httpd is (re)launched at the command line once the server has fully booted up.
All insights will be very appreciated.