I discovered that when you use "Rebuild current stage" it seems to rebuild the undergrounds one at a time based on placement order. All underground dragged in belt flow order work fine, but those dragged backwards will rebuild incorrectly(belt is fine but underground is reversed). However, once you have done a "Rebuild" then you can reverse the belts properly and successive "rebuilds" will work fine. (*I was wondering why this happened to me during play - because i had the occasional underground which got reversed in my blueprint. I finally tracked it down to the rebuild option which causes this.) This can be duplicated in seconds by dragging belt across something like another belt. Drag it forwards then backwards, then click rebuild and you will see one underground gets reversed.