I do not have the CTD problem (yet, thankfully!) But I have noticed that some roads do not make zoneable intersections, while some do.
For ex - I created a medium sized, 6-lane road using the vanilla uneven 5 lane model. I made the sidewalks smaller, added an extra lane to get 6. When I make an intersection using that road and any other road (other than itself) the 4 zoneable corners around that intersection disappear.
But, I also made a small 4 lane road using the 1-2 uneven vanilla model (also making sidewalks smaller and adding an extra lane) and every road type that I make an intersection using that one keeps the zones in the 4 corners of intersection.
I hope that makes. There are other roads I've made that don't allow intersection corner zoning and some that do, but I can't figure out why some are that way and others are not...