[eatinwokout]

Not exactly sure how to explain this so I'll paint the scenario(s):

1. I'm browsing the internet with Firefox and run accross a page worth bookmarking. I click the Ma.gnolia bookmarklet (which pops-up a bookmarking window). Normally, this window would get priority popping up in front of the browser window. Now, the window opens behind the main browser window.

2. I'm listing to iTunes and decide to start finishing some work. I click SubEthaEdit or TextMate in the dock. Normally the application window would have focus and open in front of iTunes. Now, the applications that I open do so behind the active window.

This happens with any application that I start. I usually open Dictionary really quick with Quicksilver, now the window opens behind all other windows. I've also noticed that when I open applications, in addition to them opening behind active windows, they also appear at the end of the line when I do CMD+Tab for switching between applications.

Any ideas on how I might go about fixing this?

EDIT: Just wanted to clarify that I have already repaired permissions.

[Chuckit]

Just to check, are you sure Firefox isn't always involved? Because I've seen this behavior, but somehow Firefox was always behind it.

[eatinwokout]

Possibly browser related. The same happens if I'm running Camino. Any workaround for something like this?