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The combo box selection items have a different background than the selection popup. See https://bugs.eclipse.org/bugs/attachment.cgi?id=277831
I tried to fix this issue but found it difficult. One solution is to remove "e4-dark_globalstyle.css" from "e4-dark_linux.css" and start eclipse with "GTK_THEME=Adwaita:dark" environment set. It can be avoided if "DarkThemeProcessor" can somehow call "OS.setDarkThemePreferred" before "Display" is created so that it can initialize system colors properly.
Should be tracked with Bug 563684. *** This bug has been marked as a duplicate of bug 563684 ***