Hi Pilou, could you please post the 3DM file?

Most likely though you need to swap the U and V axis directions of the base plane - in the first v3 beta Flow just maps directly from the base plane's UV directions to the target surface's UV directions and if for example the U direction happens to be going in the vertical direction instead of horizontally it could produce a different result than what you might expect.

To solve it you would rotate the base plane and scale it.

In the next v3 beta there will be a new system for matching UVs depending on where you click on each surface so that won't be necessary - see this previous post for more details:
http://moi3d.com/forum/index.php?webtag=MOI&msg=4442.24

If you post your 3DM file I can help you to manipulate the base plane to get the result that you want though - it's just a matter of rotating or flipping the plane around.

Also another issue to be aware of is if the underlying surface is larger than you might expect, see this other post for a description of that:
http://moi3d.com/forum/index.php?webtag=MOI&msg=4442.6

- Michael