I had this same problem when I recently downloaded and ran Alikiwi's update of Dermy's East Kentucky route.
It kept giving "missing junction" errors, but I couldn't see anything wrong at all.
In the end, what fixed it was moving the switches closer to the junction spline points. (after I found that, that fixed the problem the first time, I just began moving all of the switches on the route because it kept happening elsewhere too).
Everything looks normal. The switch arrows show green and red as usual, the spline points aren't flashing red, but, for some reason, the AI system doesn't like the switches being too far away from the junction (and they are an unusually long distance away on that route), but again, everything looks normal when you're looking for it.
Edit: One thing I didn't check for is if this issue is associated with a certain type of switch asset though. I.E. That particular switch type, and the distance issues combined. That may also be a factor.
Hope that helps?
Cheers,
Piere.