External programs ---Grrrrrrrrrrr

Hi all!
I have just installed my first Linux distribution (SUSE 10.0).
Everything is compiled as far as Apache, Mysql & PHP is concerned.
But, I have this problem: I call system commands through PHP using system, shell_exec etc
The thing is that PHP responds OK when it comes to 'ls' or 'grep' or 'wget', but, in another program,
not UNIX-native, there is no response.
I am sure that the program is set up in the PATH, because, if I open a terminal, I can call it from everywhere and it works fine!
Any ideas on why PHP can't call it like 'ls' for example?

**One thing that really angries me is that in the University, these things work fine, and the external program is called without any problem. *

I'm guessing this is what you were doing when you asked about the return_vars?

What's the external program you are using/calling?