Hi!
To create the reference line CadTools check for reference perpendicular to the alignment. Depending on distance to your reference and angle between alignment and reference this can be the case but it would be correct. You can easily check it by draw perpendicular lines from the reference lines vertices to your alignment segments. The displayed reference is built by points based on alignment station for the perpendicular line from reference vertex and reference vertex elevation.
If you still has some doubts, please send me a sample of your Surface file and a DWG with your alignment and reference file.
/Lars