I stopped playing this game because I always had issues with trains - wish they would fix them!

I got the same question. I tried series of layouts for my interchanges, it's really frustrating. Is there a mapping rule that bars certain layouts?

I have ran into similar issues. I decided to see if a round-about structure worked. Every time I ran into warnings like this, I upgraded all involved intersections where tracks crossed to my new flat round-abouts (without crossing any tracks!) and lo and behold: pathing worked again.

I'm inclined to say that the railroad pathing can't really handle crossing tracks beyond simple layouts.

A note on the round-about: it works, but it's ugly and somewhat awkward. You may want to look into clover-leaf intersections - I've seen some nice examples online. Those do require bridges to have been researched.