It may be that PHP (or the web server) has set up a pipe between itself and the standard output of your script. If that's the case, then PHP (or the web server) won't think the page is finished until it gets end-of-file on that pipe. When you start a subprocess, it gets a copy of your script's stdout/stderr, which isn't released until the subprocess exits or explicitly closes those descriptors.

Try closing stdout and stderr in the subprocess and see if it helps:

    $run="snmp-wdr -c mrtgtest $request > /dev/null 2>&1 &";
    echo "<BR>COMMAND SENT: $run<BR>";
    $setsys=system($run);
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