I've had this issue persisting - couldn't figure out why. But I've fixed it in two files now (haven't tried the biggest one yet) - thanks to this thread.
1. Get rid of duplicate door leafs
2. Go through every custom leaf, and make sure the parameters "coll_guid" and "coll_name" are empty, and save the part.
3. Reload libraries (and maybe reload file...but shouldn't be necessary).
If the problem is still there, then check the custom leafs again.