I don't know if it's related to a recent change in Emacs, or due to the
fact that Debian unstable now has GTK+ version 2.6.9 but I'm seeing
something odd with GTK menus: they seem to disappear every time a timer
expires.  For example, if I call M-x display-splash-screen, then open a
menu and keep it open (by not clicking on anything), the menu disappears
when the help items change in the buffer.

The same happens if I keep the pointer above a menu entry and wait for
the tooltip to appear and then go away: when the tooltip disappears, so
does the menu.

The menu bar looks like this when a menu has disappeared: