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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
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.