I've not played through the entire story line yet, never got the chance when I was a kid, but I get the feeling it might have something to do with the story. The other day I was cruising around and went to Valhalla I think, then I noticed some other jump points that seemed to have religuious/mythical references. Anyway, I followed these jumps until I came to this really strange sector that had a planet with some sort of weird-ass shrine on it, and a jump that was labeled as "unknown."
And now to the point of my little story. There was another planet besides the crazy shrine one that had a computer on it where it listed what ships were in my fleet. Of course there was only the origional Tarsus listed. I can't remember if it let me switch ships or not, I'll have to go back there and figure it out. If you find the place, be prepared to fight lots of Retros...