system and exec

I just recently did an upgrade from php 4.0.6 to 4.2.3 and several system calls that I used in my software no longer work. Both system and exec return no output from the command but if I add a '> error.log' redirect the error.log is created as an empty file. I have apache running as an acutal user login, it has permission to execute the file and safe mode is turned off. If I copy the command to run to a .bat file and execute that .bat file the command runs fine and returns the output as normal. If anyone has any knowledge why this happens i would greatly appreciate it. I have tried doing several simple examples like <? system('echo Does this work', $output); print_r($output); ?> this just echos nothing. putting the cmd into a .bat file though will echo "Does this work"; Will