Cubase 5 unwanted click over metronome .wav file

I changed the (horrible) beeps to a nice .wav real metronome click today. All was well until I shutdown Cubase. When I reopened the file was still sounding but Cubase had added a harsh click and the volume cannot be adjusted. I experimented and if I switch sounds the harsh click goes… until I shut down and reopen Cubase then the harsh click is back. Re-starting the whole PC makes no difference.

I’m recording all audio (except BFD and The Grand) so the only devices I have connected are the Focusrite audio interface, and M-Audio Prokeys Piano (which for the track I’m working on was off).

Any ideas what would cause this and how to stop it? I really find the beeps unusable but I need the click track for this recording.

Thanks in advance.