PHP in IIS 6

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I'm running PHP 4.3.1 on a windows 2k3 server. I have a script that used to 
work on my 2k server using CGI. When I use the ISAPI method under my 2k3 
server the scrip appears to work fine but when it gets to a system() command 
it doesn't do it for some reason.
Under the CGI method it gives me the  "The specified CGI application 
misbehaved by not returning a complete set of HTTP headers." error.
What the script does is it takes some data out of a database then formats it 
into a print file called "prnfile" then I use "system('type prnfile > lpt4', 
$result);" the result I get is "1". I have tried other commands in there in 
the troubleshooting process I tried "dir" and it actually give me the 
directory listing of the working folder so it appears that my code is 
getting processed. I tried "echo test > test.txt" and that did not work. 
This leads me to believe that the issue is with permissions, only I can't 
figure out what it wants. I have tried giving IUSR full permissions on the 
web folder, php folder, and cmd.exe, I have also tried giving write 
permissions in IIS to the web site.
With both methods it does create the "prnfile".

anyone have any ideas if you need any more info let me know

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