Couple comments:
- You are using an older version of Slicer. Please switch to the latest stable to get the most recent bug fixes and improvement (https://download.slicer.org)
- You seem to create individual points for your anatomical LMs, which is fine. However, you will need to keep them in a single node, if your ultimate goal is shape analysis.
- You can play with the projection distance parameter of resampling curves (Expand the advanced option). Default might be too high region of high curvature. Assuming first screenshot is the manual curve drew, almost all of it is already on the surface. If you bring it down, I think it will solve your problem.
What is curious to me in the second screen capture the start and end points seems modified. We typically assume (at least for collecting data for shape analysis) that the start and end points of the curve is fixed (anchored to anatomical LM) and then resample everything in between to generate equidistant points on the drawn curve. Process really shouldn’t modify the very first and last point on the curve.
If you want to draw additional curves in this manner, but bring them together so that they are in a single markup node (and redundant points are removed), you can use the MergeMarkups utility in SlicerMorph. Make sure you install the latest stable and get the SlicerMorph, as those updates will not be in the version you are using.
This thread (and tutorial at the end) might be also of use to you.