Monitor Not being recognized as #1

Since the Firmware update to 8.6_028 (also happens in 027) any monitor hooked up with a VGA to Display cable is read as the second monitor. Even if it is set or plugged in as the first monitor. Example if I have a Thin Client 3040 Thin OS set up with DVI to Display and another monitor set up with VGA to display. It will set up the VGA as the second monitor no matter what. It works fine with two DVI to Display.