Comment 3 for bug 879047

So I've found out what's special about these windows. They're smaller. Windows from the same application that are sized smaller disappear from the scale plugin launched by Unity.

On a lower-resolution screen I can set the "spacing" setting for the scale plugin in CCSM to 2-3 times the default and I can work around the issue. But on a higher-resolution screen such as 1920x1200, maxing out the value to 250 doesn't help.