I have this same issue ONLY when using a project template that was created in a previous version of Cubase or Nuendo. Eventually there are unexplained pops and clicks on random tracks.
If start a blank project in C8, I am unable to reproduce the problem.
I exported all my tracks as a track archive and opened them in a blank C8 project, and no more clicks and pops.
I have reported this in the issues forum, with no responses.