Just to clarify, yes this is a slightly modded install, BUT, every other mission in the game works perfectly. I have purposely made my modifications compatible with SP, and this is the only mission that gives me a problem.
The ship "SovereignR" is a refitted Sovereign that is used in SP. That ship works in every other mission.
BTW, this mission is the one where you take the Sovereign inside the Vesuvi Dust Cloud.