I recently upgraded to Ubuntu 15.10 which includes Kdenlive 15.12.0.
In this version audio in the timeline only displays the top half of the waveform as show.
Is there a way to fix this?

if i am not mistaken this is the new way waveforms are displayed, technically it is the same thing.

That's just how they look in kdenlive-15

You can revert to the old style by Settings -> Configure Kdenlive -> Timeline, and ticking Separate channels.