I had this issue before but a bit confused on your setup.
Either dual DVI + #1 display port or using both display ports should work. Your adapters might be causing some issues, which ones are you using?
Is there any reason you're not going native connections and using adapters? DP adapters are a real pain in the ass, some setups don't like DP adapters (or require the super expensive ones).
Haven't tried using a VGA monitor but I know DP to DVI should work on this card (or just 2 DP's).