I noticed an odd bug a few days ago in which the pather Starliner had 4(!) fighter bays, even though the ship.csv entry said it should only have 2. Well I finally figured out what caused it, the converted cargo bay hullmod adds an extra 2 fighter bays. Might want to replace it with your own version.
Edit: Turns out you do have your own version, but the Starliner was using the vanilla one, not that one. Also why does the Mk. IV on the Prometheus Mk.IV have brackets around it, when none of the vanilla Mk.II (or Mk.III) have them?