Are you talking about the ediff control window? Personally, I prefer it to be in the same frame as the buffers being compared: (setq ediff-window-setup-function 'ediff-setup-windows-plain).
But even when I use emacs -q and run ediff, the control frame never goes off the page, so it must be related to your Fvwm config. I doubt it has anything to do with changing focus; it's probably due to whatever placement styles you have enabled. Here is the part of my Fvwm config which is probably relevant:
,----
| Style * SnapAttraction 10 All Screen
|
| Style * ResizeOpaque
|
| Style * UsePPosition
|
| Style * MinOverlapPlacement
|
| # start on screen with pointer
| Style * StartsOnScreen c
|
| # do not jump to a desk that a window suddenly pops up on
| Style * SkipMapping
`----
,----
| # widows are focused by clicking on them
| # the focusing click is passed to the window
| # clicking in the window does not raise, but clicking on the decorations does
| Style * ClickToFocus, FPClickDecorToFocus
| Style * !FPClickRaisesFocused, !FPClickRaisesUnfocused, \
| FPClickDecorRaisesFocused, FPClickDecorRaisesUnfocused
|
| # programs can focus themselves
| Style * FPFocusByProgram
|
| # new windows/transients grab the focus when created
| # closing a window/transient releases focus to the previously focused window
| Style * FPGrabFocus, FPGrabFocusTransient, FPReleaseFocus, FPReleaseFocusTransient
`----
I don't have any emacs-specific fvwm styles. You should probably ask the Fvwm list.