There is no issue with video performance going from HDMI to DVI to HDMI - the video data is identical throughout the signal path, with no conversion applied. Don't worry about the HDMI versions for this, as the 990 doesn't support HDMI audio anyway. Also, you are correct that the 990's DVI switching is DVI-D.

If you are interested in more about HDMI, there's a link in my sig that may interest you - my HDMI FAQ.