I'm having the same issue, running at the second-highest resolution. And it gets so bad that I often can't even find the button to click to change resolutions. It's hidden somewhere behind the messed-up windows.
I'm pretty sure it's a combination of running apps, but I almost always have a lot of them open, so it's hard to narrow this down.
I had suspected that Chrome was at least one of the apps that is causing this, and today there is news that a memory leak in Chrome is causing the new MacBook Airs to crash. Could this be a different symptom of the same bug in Chrome?
Have other folks experiencing this glitch been running Chrome?
BTW: n8rand, thanks for that tip about using Automator to automate changing resolutions. It's made this whole thing bearable.