I think that something was changed recently that's affecting the positions in relation to other windows.
For me, it seems to be brought on by heavy use of the crafting skill windows (enchanting, tailoring, smelting, blacksmithing, etc).
What I do to fix it (at least the character pane, that's all I've had trouble with) is to simply first open a crafting window, then open my character window. Instead of being up in the top right corner it will move that window back down to where it's supposed to be. Then without closing anything, I move the character window to another spot on the screen, closer to the center. Then close the crafting window. After that, move the character window to wherever you want to permanently have it.
This seems to be a problem with moving any other window while the crafting window is open. It may also be affecting other windows as well in a chain reaction. Once you move a window while another more dominant window (like crafting) is still open, then when you close the crafting window moveframes tries to automatically adjust it back to where it was before you opened the window, only this is now changed and makes your character window fly off the screen.
At least, that's what I gather from casual observation.