This behaviour is erratic, and very difficult to reproduce, but fairly regular. If you have a single workspace and several viewports (I have 2x4 viewports) and exactly one window in each viewport, when switching viewports sawfish starts to select the gnome panel instead of the only present window. The result is that often you do something with applets that you do not really want (such as stopping a ppp connection by pressing RETURN). I have tried every possible focus selection combination, but this really seems to be a problem of sawfish not noticing that it should not give focus to the panel when switching viewports if there is another window.
Can you try the latest version and see if the bug is still there: http://people.redhat.com/~hp/librep-0.13.3-1.i386.rpm http://people.redhat.com/~hp/rep-gtk-0.15-2.i386.rpm http://people.redhat.com/~hp/rep-gtk-gnome-0.15-2.i386.rpm http://people.redhat.com/~hp/rep-gtk-libglade-0.15-2.i386.rpm http://people.redhat.com/~hp/sawfish-0.34-1.i386.rpm http://people.redhat.com/~hp/sawfish-themer-0.34-1.i386.rpm (This is an unstable/beta version, but should be basically OK. I'm using it.)
I have tried, but the problem is still there. It appears to happen more often when you switch from a viewport containing a big app like Netscape to a viewport containing a gnome-terminal rather than the opposite, but again since it is rather impredicible this could be a red herring... I forgot to mention that the problem appears both switching between viewports with keys and switching between viewports with the mouse.
John Harper (sawfish author) says he thought he fixed it, and requested your ~/.sawfish/custom file so he can try to reproduce it with your exact setup. Can you maybe send that to jsh? Thanks!
Forwarded upstream as http://bugzilla.eazel.com/show_bug.cgi?id=8411 Closing here.