I posted about this once before, but have some new info. Old post: http://wordpress.org/support/topic/memory-issues?replies=4
There are a couple actions we can do in wordpress to make it time out. One is trying to upgrade or install any plugin or wordpress itself from within the admin panel.
A new one today is updating a Custom Menu in the Menu's admin, under Appearance. There are about 240 items in this particular menu. Other menus don't cause this issue.
My research indicates that we're running out of ram. I've increased it several times, and I'm up to 1024 available in php.ini.
That's enough that I'm thinking there's a deeper problem somewhere.
Anyone have any ideas?