OK, so after some more testing I think I have found the issue!
The clicks happen when the decay parameter from the synth page is longer than the length of the amp envelope. It seems that when the amp envelope re-opens there is still a little signal left behind from the previous trigger. I was using the AMP envelope as the ONLY envelope to shape the entire sound, but it seems that I also need to consider the decay in the machine too. It is a little disappointing as the amp envelope shape will now be different as the 2 envelopes combined will create a different shape. It especially impacts the use of the hold stage. I will report this to Elektron as a bug, as NO sound from a previous envelope should be leaking into the next envelope. At least now I know what the issue is and I can learn to navigate around it. Not a massive deal, things still sound great 
short version
If anyone else is getting clicks simply reduce the “DEC” parameter on the “SYN” page until the click has gone. Hope this helps.