After stripping the mechanism, greasing, putting it all back together I set about testing the system without the arms for its parking position.
I decided it would be ideal to set intermittent and watch the rotation of the spindles, no intermittent wipe, but ok with normal fast and single sweep.
I decided I must have somehow spiked the electronic delay module as no joy at all with intermittent and resigned myself to a car with no intermittent wipe.
The following day I searched the web for Polo 9n loss of intermittent wipe and found a post explaining that VW design the wipe system to isolate the intermittent wipe when the bonnet is up
I can confirm that this post was right. My intermittent wipe does in fact work with the bonnet down and the clicking sound has gone.