This evening i've done some more testing. I created some .esl and .esq files using Ekos (the ones above I generated in excel) and the same happens.
The first was 4 targets = 600 images. Then I added some more targets, saved it down and ran again. But after 5 images it failed (so 605 images successful since EKos was started).
I then started it again and if my maths are correct it has failed again after another 605 images. Feels like too much of a conscience. Is Ekos keeping some sort of log of what it has done as I note on EKos restart scheduler knows how many images it has taken of each target or is it scanning the image directory?