Sorry for the delayed response - but can you provide me more information about your configuration? Are you connecting directly from your system to the projector, or is it going through a 3rd-party device such as an AV/R or KVM? Are there any adapters/dongles being used?
When you say the wrong colors are used depending on the connection, can you provide more detail on what the colors and/or other symptoms are per connection type?
Lastly, can you provide a copy of your dxdiag? (Start -> Run -> dxdiag -> Save All Information).