Just to be clear: Do you have a dual-output card, and a dual-input monitor, and you have both card plugs connected to both monitor plugs? If so...
Most likely, the LiveCD, for whatever reason, was configured to enable both video card outputs (each is configured as a single video card, basically) but with your hard-disk installation, that configuration is not in effect by default. As a result, only ONE of the video card outputs is being enabled by default. That is normal.
You would need to specify in your xorg.conf file, a device section for each card output, as well as a monitor section for each monitor connection. Probably also, you would need to have an extra "screen" section, for the second card+monitor combination.
I have a pretty much very similar setup, with dual-output nvidia cards and Samsung 2243WM monitors, and all is well doing what I describe above.
If you need help configuring your xorg.conf file as I describe, first do a search for a thread in the HARDWARE forum, posted by me, which lists a bunch of xorg.conf examples I have used over the past few years, for clues as to what you need in your file.
If I've missed the point of your question, my apology; please explain again in more detail if I have