Many people have have pointed out the difference between `` and system(), but I'd like to suggest that the problem you're seeing might not be something you need to fix in your perl script. The problem might be that in upgrading your RetHat distro, the program(s) you are executing using system() may have changed, such that if they detect they are running attached to a terminal, they wait for input on STDIN. (and in the old version, the program may not have assumed this).
It's also important to remember that system() adn `` can/will pass your input to "/bin/sh -c" if it contains shell metacharacters, and on many newer systems /bin/sh is just a symlink to /bin/bash -- which may also be why you are now seeing a different in the behavior of your script. Your old distorbution may have genuinely had "sh" installed, which may have involved your program(s) differently so that they didn't know they were attached to a terminal.