I had this exact same problem, and it had me really confused for a while. I had a brand new WordPress 2.9.2 installation, no plugins, nothing. The admin menus were indenting. See example.
I found this was only happening in Firefox 3.x, and then I realized it was because it was zoomed.
In Firefox, go to View -> Zoom -> Reset, and that should fix it. Worked for me.
