If I disable theming for the PyDev Package Explorer, by unchecking "Apply to all (non-Studio views)" in Apatana Themes, I'm still getting problems with fonts and colors. In this case, most of the entries look unthemed, but some of the files, have the background from the theme and a foreground color not taken from the theme. For instance, some files have the background color of dark brown for "unstaged files" from the Aptana theme, but a foreground color of grey or black that makes them unreadable. The themed color for "unstaged files" should be white.