OK I don't think this was mentioned.
Is there a metronome buss?
If not insert a new buss in the buss pane and name it metronome. Make sure it outputs to you interface or Master.
Now go to the metronome dialog and make sure this is the output.
Don't forget to click apply after making changes.
I have no clue why toggling the effects bypass works but every time I have your issue, which has been many,, it has worked Note. I always do this ( toggle effects bypass) on my MASTER buss bin.