IntelliJ IDEA 12.0.2
The colours used for the highlighting make the code fairly unreadable when you use the new dark colour scheme of IDEA 12 (Darcula). See attached screenshot for how unreadable it becomes. Of course, the default colour scheme works as you expect.
Open "File -> Settings -> Project Settings -> Clover". Open the "View" tab. In the "Source highlighting" panel click on "Uncovered / Failed / etc" checkboxes and select appropriate colours (the dark ones from second row from the bottom look good). Click "OK".
To be implemented:
Prepare two sets of colours (for Default and Darcula schemes) for highlighting. Clover should detect which scheme is the active one upon start-up and select proper highlighting. In case user has different colour set, he could always define Clover's colours manually as described above.