The Click in Mixbus (OSX) randomly misses beats. I am currently using 2.0.2. I don’t know if the same thing happens in Ardour. I will test that but once again I had to abandon using Mixbus because of a simple problem.
You should report such issues to Harrison, via the email address you will have got when purchasing Mixbus. Also, you are a couple of versions behind, so I would suggest you update and try again first.