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I use two displays - a 26 inch monitor and my HD TV on my Geforce GTX 295. Unfortunately, Vista seems to want to force my HD TV to be the #1 display and my Computer Monitor to be the #2 display. The Geforce control panel does let me specify which is primary but regardless of what I specify, some programs including keyclone just assume #1 is the primary display. It's awfully annoying. Is there anyway to specify which is #1 and which is #2?
Have you tried switching the ports they are plugged into on the back of your card?
I presume you've rebooted after changing primary monitor?
It's not Vista's fault, it's up to the video drivers. That's made obvious when you do a driver update and your primary display is mysteriously reversed (which happened with my nvidia cards a year or two ago)
Anyway, software won't necessarily determine which is your primary monitor. Some software, perhaps including Keyclone (couldn't tell you), will use the monitors in the order Windows lists them (as given to it by drivers). Switching primaries in Windows will not affect this order, instead there's a flag set on that monitor in the list that software can just ignore (perhaps the developer wasn't aware that he might even want or need to look for such a thing).
To switch the monitor order, just switch the plugs like muffin suggested. Then change the primary in Windows again if needed.