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Setting Java editor's background to black and "others" to white makes some elements invisible in the compare view. This was noticed in team plugin synchronize view using 20020425 build, but I think this is a compare problem.
*** This bug has been marked as a duplicate of 14680 ***
I don't think the bug is a duplicate, although it might be related. The other bug complaints about detected change highlight color, while this one makes some elements invisible even in areas with no differences. Also, java editor background may or may not be the same as system color scheme background color.