I advise against the use of 'tools' to manipulate your chameleon configuration, it's better to understand what exactly is going into your boot.plist in /Extra and not very difficult to manipulate. There is absolutely no reason to enable or force 64bit on an intel system, as long as you do not have arch=i386 in your boot plist you will be running a 64bit kernel. Judging from what you have mentioned I would suggest that you probably don't need anything in there except EthernetBuiltIn=Yes and GraphicsEnabler=Yes - though you may want to play with PciRoot=0/1 to see if it helps anything graphics related.
Have you tried connecting the displays directly to the 9800GT? I have noticed myself with my 9800GTX+ that one port is initialized at boot time, and the other displays after login - I do not use mirroring. Disable mirroring and plug them directly in - check graphics init order in bios, check your PciRoot=0/1 these are the first things I woud suggest trying. If tampering with none of the aforementioned helps your situation then yes it is most likely an issue with the graphics enabler injection on your particular 9800GT - in which case you may need to define the outputs and injection manually in dsdt.
I hope this information is helpful, good luck.