Hi Andy, if you've got a circle there you can just rotate the result around the circle's center point or rotate the circle before doing the Flow.

Another option would be to trim open a small empty spot on the circle so it's an open curve, then you can match it by which end you click closest to when selecting the base and target curves.

You can also use this plug-in to relocate the "seam" for the start point of a closed curve:
http://moi3d.com/forum/index.php?webtag=MOI&msg=10125.8

- Michael