Hi Brian, actually I had thought that you were using curve-to-curve flow.

Surface to surface flow is done by mapping "position in UV space" from one surface to another, it does not necessarily map from distance to distance because UV space is not necessarily uniformly distributed, a squishy surface can be narrow across in one area but wider in a different area of the same surface.

If you are dealing with extrusions then that's a particular case where they are uniform, but also if you're dealing with extrusions using curve-to-curve flow should just be easier in general.

Check out here for an example of using curve-to-curve flow for this sort of "height mapping" from one 2D profile onto a bendy curve:
http://moi3d.com/forum/index.php?webtag=MOI&msg=4785.13


Or here's another example - here is an angled line with a base line under neath it:



Select that angled line, it's the one you want to remap onto the bendy curve. Run Transform > Deform > Flow, select the base line underneath it as the base curve, and the bendy curve as the target curve and then you'll get a result like this:




Initially the curve will occupy the same length of the target curve as the length of the base line. You can enable the "Stretch" option (which I did here) to make the result stretch across the full length of the target curve.

But curve to curve flow works by traveling across curves by distance traveled along the curve, surface-to-surface flow uses the UV parameter space of the surface which can be compressed or expanded in different zones of the surface and so if you want to do stuff that maintains distances the curve-to-curve flow may be better.

- Michael