Sounds like your display cabling is wrong. Do you have a pic of your display cable connections at the brainbox and where it goes on each display?
If you don't have the add on E4690 video card. Do you have a DVI>DVI cable connecting to the top display and a VGA>VGA cable to the lower touchscreen display?
Or if you have the add on video card which has dual DVI outputs. Is the top DVI port going via DVI cable to DVI on the top display, and does the the lower DVI port on the card have a DVI>VGA adapter and then connects by VGA cable to the VGA port on the lower touchscreen display?
If you have the add on video card that's dual DVI. The top DVI port can go to anything, even converted to HDMI. But the lower DVI port always has to be converted to VGA and connected to the touchscreen with a VGA cable. Even if your touchscreen happens to have a DVI input as well as VGA. Otherwise the machine gets confused as to which display is the primary touchscreen.