Have you checked the options thoroughly? I dock with different monitors and I seem to be doing okay with the option I have selected (shown the graphic below). Full disclosure -- my resolution isn't vastly different on my monitors like they are on yours. I would test out each of those three settings provided.
Where 3d desktops have failed, this app has shined. Best organizational/productivity tool since I discovered Trello. Now my problem... Given the different environments I'm in and roles I have to play, there are quite a few dashboards/launchpads I'd like to build using Fences. I'm quickly finding that putting together screens of fences is becoming a little unruly. I find that I need to create some different fences for new aspects to a project/client, but now