I've had this problem with every version of windows that I remember since I have been putting the taskbar up at the top of the screen. Why Windows has never been designed to properly use this setup is beyond me. In fact it is by far more productive way to have things with the taskbar up top.
Anyhow I have fixed this "error" every time but I cannot recall how it was done before.
Typically to fix it temporarily I move the taskbar, move the window in question down and move the taskbar back. This isn't very productive. Most programs should remember their position when closed, but apparently aren't remembering. There should be a way
to force windows to open on top of the taskbar. I know I could auto-hide the taskbar but I don't wish to do that.
I am using Windows 7.
btw I did a search but did not find anything like this, but perhaps it is worded in a very strange way lol.
There is a custom solution here: http://www.sevenforums.com/customization/44913-disabletaskbarontop-disable-taskbar-always-top-9.html But for all practicial reasons, this is a 'by design' feature in Windows 7.
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Sorry this didn't help.