I don't get why the screens sometimes swap around. It makes no sense to me that sometimes when I log in, my extra screens are switched and I have to move all the contents. The machine has the serial numbers of the screens, and it knows what ports they are connected to. Why can they not just use that information to remember where stuff is supposed to be? The other thing that annoys me is that it changes the background…
Found this from a post here on HN a few weeks ago, but apparently manufacturers of monitors don't bother to give the monitors unique machine ids, except in batches. Since everyone's two monitors are almost always from the same batch, they can't be told apart on a hardware level. I thought I had struck paydirt in that HN post (a tool that helped with this), but since the two monitors of mine aren't plugged directly into the Mac, the tool can't fix it for me. It would have to somehow work on the level of the docking station. If I didn't have bad luck, wouldn't have any at all?
But it's so much worse than you describe. In theory, I should be able to hit F3, see the little "desktops" at the top, and drag the one from the left monitor over to the right, and then vice versa. But somehow, there's always one virtual desktop that can't be dragged in this manner, and it's always the one with the applications.