It happens on multiple system calls. One example is running ps2pdf12 to create a pdf from ps file, in that instance I am not capturing stdout or stdin. In other instances where this error occurs I am capture both (running using backticks and redirecting stderr to stdout in the command).
Have not tried proc::background, or strace, so will try that. Also read Apache::SubProcess might be worth trying so I will also attempt that today.
Will report back if anything works.
Also read last night that including Test::MockObject was creating a similar type of error for somebody: http://www.apache-httpd.com/list/39/962672.html.
I was not including that module but did have Test::More, although I tried removing Test::More and it hasn't helped.