Thank you for the reply. I think (as usual) this was my own doing. I think I should have just started a fresh sequence that didn't have the autoguider enabled. The sequence I was trying to run did have the PHD2 guide camera connected - so it was always looking for settling (I was dithering). So in the future I will have a "basic" profile that does not include guiders/filter wheels etc.
On another note is there anyway to disable the "end of sequence" dialogue as I never want it to run any shutdowns of anything?