This is addressed here: http://askubuntu.com/questions/70599/how-to-
change-tooltip-background-color-in-unity
In short, a workaround (until this is fixed) involves:
1. install unity-tweak-tool: sudo apt-get install unity-tweak-tool
2. run the tool, and modify the theme to something else ("Highcontrast" and
"Adwaita" themes work for me).
Also in the askubuntu link above, it is mentioned that you can manually
tweak aspects of individual themes by making modifications to files
within /usr/share/themes. This might be more work, but allows you to
use your preferred theme.
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https://bugs.launchpad.net/bugs/1332100
Title:
Colour combination makes qt tooltips unreadable in Unity
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