I cloned the route and I'm going through all the trouble sections, one of which is New Bridge Landing, where the track is set to "up/down" direction instead of "Both". Changed that and now I can pass through that section. There's also an area between Secaucus and Wood Ridge before the other track merges in that Y-intersection (if that makes sense). I'll keep messing around until I can find the other problem parts, and report 'em here.