I was trying to decide which way to to sync the prologue and the Minilogue, in the end I went with the Minilogue being the master (sync out) and Prologue the slave. The deciding factor was the tempo knob on the Minilogue, it is a lot easier to use that for the tempo than the button on the Prologue.
Anyway after setting it up this was with 16th note timing the oscilloscope freezing I used to see on the Prologue when using the arpeggiator has now gone away and it is behaving normally.
As a test I might plug the sync out on the Prologue to it's sync in and see what that does... hopefully it won't blow it up like searching google on google crashes the internet