Thanks guys, you got it spot on.
Although the whole workflow is progressive (the sequence settings and all clips in the browser are set to field dominance ‘None’ & AE field render is off) I went through the whole timeline checking the item properties of each clips individually and found the culprits, FCP had interpreted the clips with animation codec as upper field first.
So change that, force a refresh and all the edges are pristine.
Thanks again, as very tired and no time for whole re edit before deadline!
Sean
Sean Vicary
http://www.seanvicary.com