I have used the system function without problems
I think the only thing you are missing the path to the program.
I use system to backup my MySQL databases using the following code:
$date = date("Y-m-d-i");
system("c:\mysql\bin\mysqldump mydbase > $date_dbase.sql");
and then i even did a floppy backup, just in case my Hard Drive goes bum...
system("copy $date_dbase.sql A:");
it works for me.. in windows 95,98,2000 professional...