[Brian]

Another customer identified a bug today which I suspect is what you ran into: it happens when you've got a window open which includes a perspective and that perspective is focused on some set of projects/contexts. The "Show All" or "Revert to default view" commands are used.

Here's the bug: even if you subsequently point this window at another one of your perspectives, the preferences don't get updated properly. Close that window and open another one, and you'll get a window that's pointed at the "Show All" view.

This has been biting me occasionally for a while now, but I never managed to figure out exactly what caused it. I owe the user that did a cookie. :-)