In "cross-eyed" 3d mode, in order to select an object, you need to put your mouse over where it would be if it were full screen. This makes it confusing, since you don't actually place your cursor over the object, you just have to guess where it was.
To understand what I mean, make it so a small object is on the right side of the screen, and try to select it using the left box.
Anyway it could be made that we click on what we actually see, not where the planets are on full screen? I can't stand the false-color of the color glasses...
I hope you understand what i mean.