I could solve this problem by adding the following lines to the file
/usr/share/themes/Clearlooks/gtk-2.0/gtkrc:

style "clearlooks-tooltips" = "clearlooks-default"
{
        xthickness = 4
        ythickness = 4
        bg[NORMAL] = { 1.0,1.0,0.75 }
}

And later in the same file:

# tooltips stuff
widget_class "*.tooltips.*.GtkToggleButton" style "clearlooks-tasklist"
widget "gtk-tooltips" style "clearlooks-tooltips"

See the gtkrc file for the Human theme (I copied from there).

It did not only affect the tool tips and notifications, but also for
example the bar that is displayed in Firefox when a popup is blocked.

-- 
*new* usability bug with clearlooks
https://bugs.launchpad.net/bugs/107943
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