Comment 6 for bug 461335

well I'm sorry but you didn't reply for 3 weeks so I thought the problem was over.
If you deactivate the taskbar in the Dock, without restarting your gnome-panel, windows will of course continue to minimize to the dock, because windows are bound to a position on the screen, and not to the panel or the dock.

Morevoer, it's strictly impossible for the dock to set the position of the minimized window if it does not act as a taskbar (you need at least the X ID of the window to do that, and the dock doesn't record them if the taskbar is not active)

So I maintain this bug invalid, except if you can provide more details and a way to reproduce it (because I just don't have this issue on my PC).