Yep, just keep the config and show it to one of us (maybe just attach it here, or open an issue on googlecode).
Does this only happen on x86/32bit? Never happened to me XD
Is this bug fixed in rev 6286?
You'll need to correct it yourself the first time, but it shouldn't repeat itself. (i think)
You don't really need to delete Dolphin.ini, you can just change the lines
MainWindowPosX = -32000
MainWindowPosY = -32000
to
MainWindowPosX = 0
MainWindowPosY = 0
That should correct the bug and don't mess with your configurations.
Happens pretty often acually if the games crash or if you like to exit with alt+f4.....
Solution:
RightClick on "move" on dolphin in the taskbar
Press and hold "windows key"+Arrows to move the window around
(at this point after moving it a cople of times with the arrows the window will snap tho you current mouse position)
and there u have it.... hope I helped