G'day Josh,
For what its worth, I've seen similar scenarios many times while in the (ongoing) process of developing a design environment for OpenRoads. It is frustrating and very finicky.
Like I wrote only moments ago to the guy who is helping me (he is only an hour into his day and already seriously frustrated)... "small steps grasshopper".
It seems that the setup must be perfect before begining a design or else you'll see what you have seen.
And repairing the libraries and thinking that an "update" of the design should fix the design (which I'll admit is a logical thought) just does not seem to work.
You make the fixes to the libraries, and start the design again.
Then it works. At least, up to the point where you find the next piece that is not quite configured correctly.
If one thing is clear to me, you'll need a bullet proof design environment before begining to use the software in earnest, or it will be a very frustraing process for the designers.
Small steps grasshopper
:-)