I don't shoot AVCHD, but I downloaded some a couple of years ago and I don't see the problem you are seeing. So maybe you need to get more specific?
I put the source clip in the Source Monitor, and using In and Out points, I dragged three different sections to the timeline. I then made a subclip out of each of those. I then put the subclips into the 2X2 array with a second clip that is also AVCHD.
Perhaps what you used for the vignette is fouling you up? How did you create it?