I've found that practically any problem will cause an AI train to report "junction has missing lever" when it can't plot a path to the next marker. That includes weird things like track that somehow overlays another track with the marker on the wrong layer, or track direction markers facing the wrong way, it reports "missing lever" simply because it can't find the path and assumes that must be the cause. Troubleshooting that type of thing takes time, best done by placing a string of track markers every 100 yards in the suspect area, then closer together as you narrow it down. That's if you can order the AI to abandon schedule and drive the path yourself of course, that's the first thing to try and if you derail you've found the problem. If you can run the ordered path without derailing, then you look for missing levers or direction markers facing the wrong way, if you don't find any then you go to temporary track marks.