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Yes it seems that it uses SELINUX
That explains a lot.
Selinux provides "security contexts", and everything that a webserver may run is in the server's security context.
This means that it is not allowed to do a whole lot of things, even if the file permissions allow it.
Which in turn means that virtually everything can go wrong.
I'd recommend to write a daemon that runs a normal user, validates it input and executes the program. The CGI script and the daemon can communicate via TCP or named pipes.
In reply to Re^3: System and CGI - File Created but not the Content