@Neil-Bartlett, I have seen the scrambling of waypoints often, I suspect especially Basecamp exports suffer from this, but I don't use that anymore so I cannot say for certain. MRA imports these WP's in the order they appear in the file. Some software seems to export them in a numbered order not following the same logic as MRA uses. WP10 can appear before WP2 in the ordering in the file. Usually it can easily be re-ordered using the left column.
Then there is the very common problem where the created route does not completely comply to the track. That is quite logical, because who knows what routing logic was used to create the track, and on which map it has been done. Did they use shortest or quickest, avoid toll roads, maye even traffic info interfered with the course of the track... You will have to add waypoints to make the route compliant to the track.
Usually I import both the track and the route. I then take a look at the waypoint info, to see if there is any sensible info in them. If they are just placed waypoints with no further extra info, I delete them all and start drawing my own route using self-placed waypoints.
