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I had this once, the windows were opening on a different screen. It wasn't even a physical screen (I do have two, but the second is mirrored as it's in a different room), it was a 'virtual' second screen off to the right. It's not that is it?
I don't think I could two finger swipe using my magic mouse to see the virtual second screen but when I went to displays in system preferences and got everything back onto one screen the problem went away.
Fox-
Do you mean spaces? ( I think that is what apple calls it, where you have multiple desktops which you scroll between) if yes then I use them frequently and I'm sure it isn't opening in one of those as it doesn't show up at all.
When I minimise the window to get it to appear, it shows the animation of it moving from a spot on the desktop to the bar at the moment, so it is there but just invisible
haveo
Anyone had any problems where when you open an application, no window appears but the program is running? I had this a long time ago with photoshop on my old macbook and I have had it for the last month or so on my new mac with system preferences. The only way to see the window is to minimise the program and then when you click back onto it, it appears. Its strange, don't know what causes it.