Just to clarify, I know how to set up a dual monitor system. For 5+ years I've had 2 22" set up via dvi, and before this, had one hdmi 27" and one dvi 22", it's when I set up both as hdmi that I'm having the issue.
I haven't heard back from their support. I switched the HDMI on the second monitor to a DVI and they are seen as two monitors. I'm inclined to say that they cannot be run both as HDMI without being duplicate or one big monitor.