Hi Colin, that happens when the u and v directions of one of those surfaces are swapped from what you want.

Right now the Flow command just maps from one UV space of a surface to the natural UV space of the other surface and doesn't yet have any options for controlling how they should be matched.

At the moment the easiest way to deal with that is to re-arrange your plane - squish your plane so that it is long in the other direction and then rotate the plane 90 degrees (and possibly flip it) and that should get you what you need.

That won't be necessary in the next beta though - in the next beta I've added a way to control how the UVs will match by paying attention to where you click on both the base and the target surfaces - you'll click next to an edge near one side of the edge, and then click on the matching spot on the target surface and it will then swap and reverse UVs as needed to make those spots be aligned.

So this problem should get better in the next beta - you'll just have to pay attention to where you are clicking on each surface.

- Michael