I've solved my own problem!

I keep a rubbish bin of groups and objects I've finished with but which may be useful later.

I still had the Nurbs circles I lofted to make the body in the bin!

I selected each Nurbs Circle one by one, and rotated them on their local axis by 180 degrees. I then relofted and voila! I had the seam on the bottom.

I'd still like to know how to fix this, as it will likely be a problem in future, and I may be unable to just pull the circles out of the bin.