First, you aren't checking the response code of the program. You don't know if it failed to run. Also, there should be some error ouptut if it fails. Where is that going? Things to check are different permissions and environment variables between the apache and shell user.

Also, I don't like using the backtick operators in void context. If you aren't capturing the output in a variable, it is better to use the system function. One advantage is that the output isn't stored in a possibly huge variable; it is sent straight back to the web server. Another is that the return value can be checked. Finally, the array form of system can be used to bypass the shell.