Hi Trees,
I wonder if your problem could be related to this:
http://www.ddwg.org/lib/Dual_EDID_guide10.pdf
Apparently the EDIDs for the digital and analog part of a DVI interface may be different, but they are polled through the same DDC pins. If the monitor is connected with a DVI-I cable the computer side may not know which one it is getting. They suggest using a DVI-D or a DVI-A cable as a workaround.
In your case the HDMI-DVI connection should work, since there's no analog part involved. Changing the other one to use the VGA would force that one to use analog and might fix it, or use a DVI-I to DVI-D dongle if there is one, or if you are adventurous just snap off the analog pins from the connector. The pinouts are here:
http://www.interfacebus.com/Design_Connector_Digital_Visual_Interface_DVI_Bus.html