Oh, I think I have an idea of whats happening and how to fix it
Nope, can't reproduce.
What I did (with Editor Extensions Mod):
- Run new game with FIB disabled
- Placed some ghost inserters by hand
- Copied BP from my library to inventory and placed it in world
- Save game, quit.
- Enabled mod
- Made construction robot build everything - eveything works as expected to me, all inserters in blacklist mode
- Just to double check - placed BP again, robot built it - still everything fine, all inserters in blacklist.