(FYI I've been playing with the newest version of MediaVPs 4.6, FSPort MVPs 4.6, and STR)
On the mission "Return To Ross 128" your default craft is the Loki. However, if you play as that you are flying the older model of the Loki and not the newest one recently introduced. The weird thing is, is that the enemy Lokis in this mission are the newer version of the Loki...so the enemy has the most recent version, but not the Loki that the player flies.
Could this be fixed?
(P.S.: The mission is playable and beatable, the player just has an older model than they should.)
(Another FYI: I haven't got there yet on my campaign playthrough, but I tested the final mission (destroy Hades) through the techroom and in that mission if you select the Loki to fly, you fly as the current Loki model...so it looks like it's a particular mission problem.)