Hi nickrose
Certainly not a silly question in this instance. You are absolutely correct. I had the guitar going into input one and output connected via output 2. My bad! Bypass is now working fine.
That'll teach me for tying to fiddle with my signal flow at 3 in the morning!
Thanks for your response. Time for me to put on the "noob" hat! 
I look forward to learning more about what this pedal can do.
Dan
