Hi Martin & Burr - so with a surface-to-surface flow the particular orientation of the objects does not really matter (whether they're on the world "Front" plane or on the world "Top" plane or whatever) - the one that you're thinking of Burr was a problem in the first v3 beta with curve-to-curve flow (curve backbone to a different curve backbone rather than surface backbone to surface backbone), but that should be fixed now.

However, with surface-to-surface flow the spot that you click on each surface is significant, so you will get weird results if you do not pay close attention to making sure you click on corresponding parts of the base surface and the target surface - it will rotate your shape to match to the spots that you click on and if you don't click carefully you can introduce improper rotation.

Check out here for a description on the pick areas:
http://moi3d.com/forum/index.php?webtag=MOI&msg=4795.10
http://moi3d.com/forum/index.php?webtag=MOI&msg=4442.24

This should get better when there is a proper help entry for Flow.

- Michael