I have experienced this in both Animate Pro 3 and Harmony Premium 12.1.1 When I create a custom line for the Polyline Tool the saved characteristics do not apply to new lines. I will open the Polyline Tool and select the custom line preset. The Tool Properties related windows display all of the characteristics I have assigned to the custom preset. However when I use the Polyline Tool to create a line the line is a basic line without the customized characteristics. The only way to get that Polyline to exhibit my special line characteristics is to use the Pencil Editor or to use the Select Tool and then to click on the custom line options. A factor that may be of significance is that my customization includes a texture. All of the textures seem to behave similarly whereby they do not initially apply to new lines.
EDIT: I now believe the texture may be the only element that is not applying in these customized presets. The size and smoothness information appear to be consistent with my customized settings.
I am also aware that the User Guide states, “Textures are independent from pencil templates.” This should not prevent them from being assigned to a custom brush when the option is included in the Polyline Tool Options editor.