I have had a similar problem in the past, with my MBP 15". I would hook it up on my dual screen, and every time I plug it in, it would be different. Have you had experience with other Macs on doing dual monitors?
What happened to me is, eventually, it starts to remember it. Before, the arrangments would be off or reset, and even my wallpaper for the dual monitor isn't correct. Are both monitors always plugged in? It also could be a possibility that the cable is loose? Or adaptor part.