For non-C development, there are other files setting it:
a...@flower2:~/projects/.metadata$ find . -name *.prefs | xargs grep 
sourceHoverBackgroundColor
./.plugins/org.eclipse.core.runtime/.settings/org.eclipse.cdt.ui.prefs:sourceHoverBackgroundColor=245,245,181
./.plugins/org.eclipse.core.runtime/.settings/org.eclipse.cdt.ui.prefs:sourceHoverBackgroundColor.SystemDefault=false
./.plugins/org.eclipse.core.runtime/.settings/org.eclipse.dltk.ruby.ui.prefs:sourceHoverBackgroundColor=0,0,0
./.plugins/org.eclipse.core.runtime/.settings/org.eclipse.dltk.ruby.ui.prefs:sourceHoverBackgroundColor.SystemDefault=true
./.plugins/org.eclipse.core.runtime/.settings/org.eclipse.dltk.ui.prefs:sourceHoverBackgroundColor.SystemDefault=true
./.plugins/org.eclipse.core.runtime/.settings/org.eclipse.dltk.ui.prefs:sourceHoverBackgroundColor=0,0,0

And the last two (Ruby and DLTK) get reset after shutting down Eclipse,
even though I've set it to the same as CDT.

-- 
eclipse: tooltips unreadable
https://bugs.launchpad.net/bugs/540332
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