We ran into a problem where AutoMapper changed it's approach between versions for a way we were using it. We then got to spend the next few weeks updating our code because of it. I'm pretty sure that all the time we "saved" by using it was lost.
My project had the same issue. I ended up stripping out AutoMapper and manually mapping my types. In the end, it was much easier to determine exactly what was going on, and now I have one less third-party dependency.