Sorry to thread dig, but I had the same issue which I resolved after some research and will help some peopole. For 2560x1080 monitors in Skyrim, you need to change the iSizeH to 1080 and iSizeW to 2560 in the SKyrimPrefs as Dragoon mentioned. This will make the resolution sort of fit, but will cut of part of the screen (especially with SkyUI). I've tried various changes to the resolution height to fix it, but it still ends off with cut off content or letterboxing. You then need the FlawlessWidescreen on top of that from Swede's post to correct the scaling of the image. It will detect your game when you have it on, and it will even support SkyUI, which was the main issue after changing my resolution. Now my Skyrim looks most excellent. I may have to tinker with FOV settings though.
I'm probably going to end up donating to FlawlessWidescreen because they fixed an issue that developers are barely noticing. It's a bit First World Problems, but it's annoying to have a superior PC that can't play games in fullscreen at the native resolution (went from having a ♥♥♥♥♥♥ computer to one that is too good). I often have to play games at less than native resolutions.