Are your screens different size?  http://www.nabble.com/Sawfish-Gnome-
Xinerama-dropping-windows-t4652994.html seems to be about this problem,
too; alas, no actual fix in sight yet.

If the windows are simply placed outside the screen (a plausible
hypothesis given the symptoms), can you use sawfish-client to move them
back where you want them?

(I'm not on a Sawfish machine at the moment, but I'll happily post some
Lisp snippets when I am.)

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Windows disappear from desktop, but continue to run
https://bugs.launchpad.net/bugs/49740
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