My Eclipse seems to have a problem with the themes. I use the standard dark theme that comes with it and I also use a color style to change the background/text color. I have the Luna version.
Even though it does accept the changes if I hit "Apply" and "OK" when I restart Eclipse it seems to ignore the changed color style. The same happens if I change the specific "Java Editor" settings...gone. I do NOT change workspaces or something like this... Any ideas are welcome, I can't stand the color pollution of the default theme. :(
Try this (for me the problem was a collusion with c++ development plugin - but it should solve it):
Moonrise".Then go to Appearance > Color Theme and select your theme
For themes to be available follow this: http://eclipsecolorthemes.org/?view=plugin
Note the difference between Color theme and Appearance Theme