I found that with disabling stream blocking I was sometimes attempting to read a return line before the external application had responded. So, instead, I left blocking alone and used this simple function to add a timeout to the fgets function:
// fgetsPending( $in,$tv_sec ) - Get a pending line of data from stream $in, waiting a maximum of $tv_sec seconds
function fgetsPending(&$in,$tv_sec=10) {
if ( stream_select($read = array($in),$write=NULL,$except=NULL,$tv_sec) ) return fgets($in);
else return FALSE;
}
