The GTK+ theme "Indubstrial" is now the default in GNOME 2.8. One thing it does is to use a lighter background colour inside notebooks (GtkNotebook) and group boxes (GtkFrame). Here is an example of a correctly rendered GtkFrame:

Here is what happens in Eclipse. The contents are in a composite control, which is given its own X Window and therefore inherits the default background colour:

Here is an example of a correctly rendered GtkNotebook object:

In eclipse, only the tabs themselves get the correct background colour: