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In the default theme on Ubuntu 10.04 tooltips are shown with black backgrounds. This is the colour that the javadoc view and javadoc hovers use, and WebKitGTK's default links don't show up too well, they're a bit too dark for the black background.
The link colours are actually fine, there's a WebKitGTK bug with resolving the InfoText color style. Have logged: https://bugs.webkit.org/show_bug.cgi?id=41296 with WebKitGTK. Closing report.