As stated above, it needs to go from the top left corner to the bottom right corner. Just use this to flip it if neccessary:

// flip them if neccessary (x3, y3 are temp vars)
if($x1 > $x2) { $x3 = $x2; $x2 = $x1; $x1 = $x3; }
if($y1 > $y2) { $y3 = $y2; $y2 = $y1; $y1 = $y3; }
ImageFilledRectangle($im, $x1, $y1, $x2, $y2, $color);