I did some test with both prefabs and copypastes, and it works for me (including rotations, and copying a footpath + moving along an axis causing the copy to be parallel to the original), but I did notice a bug - if you don't press "enter" to finalize the path data before saving a prefab file it gets saved in an incomplete state. This might be what's happening here?
The only other things I can think of is if the origin coordinate calculation gets messed up when you load the prefab with the marker size larger than 1x1x1 or if there was some funky interaction with you having something in the copypaste buffer already when loading a prefab - does it behave as expected if you press "alt" to quick-reset the cursor before loading the prefab?