I every case i've ever heard of a dual image is 480p/31kHz on a 15kHz monitor. So Retroarch must be grabbing 640x480@60p somewhere, and this should not happen if you set things up right. As Paradroid asks, what shows up in ArcadeOSD? Have you set EDID emulation on and installed all the modelines you need, and can see them in the list in ArcadeOSD? When you lock system modes, can you see anything you don't want in the list?
Have you stopped and disabled the AMD External Events Utility service? And ticked hide modes this monitor cannot display in display properties in windows?
Also, search for retroarch threads in this subforum. I know very little about this, but IIRC RA used to have issues switching from progressive to interlaced and vice versa, but i think they're working on that. Not sure if it's a fork or what. So if you're not using the right build you won't be able to go from a 480i desktop to a 240p game easily?