We had the same problem. We ended up having to take Lucee out of single mode and that resolved the issue. Next week I will see if I can figure a way to duplicate it and share the results.
In my testing, I was able make things work by clearing the caches in the admin area in a specific order. It would then work for a bit until both sites applications were loaded.
I wasn’t able to find a pattern as to why, but some cfcs would load correctly, while other CFC/functions would load from the other site.
I know this wasn’t exactly helpful in figuring out what is going on, but wanted to share my experience.
I see there is a test suite for this. Single Mode Test Suite I will expand on that.