In IORegistry, check the connector-type on each AppleIntelFramebuffer object. 4 is DP, 8 is HDMI. I don't know which is DVI.
If the connector-type is wrong, you need to add KextPatch for each port to the right connector-type. Download sample config.plist from
here. It has patches showing how change each of the 3 ports from DP->HDMI (4->8), however, you need to change the patch strings to change 4 to the right type (8 or DVI type).