Okay, just to confuse things a bit more...

Right now, everything works as it should - in-game. But, strangely enough, when I activate Mod/Derelict, the Tech room ceases to show certain ships. Actually it only shows no Shivan ships, and many of Terran and Vasudan ships also are missing from Tech room. For example, only the following Terran fighters and bombers are present: Hercules, Loki, Myrmidon, Medusa, Ursa and Zeus. Not much, eh? However, Perseus, Herc II, Erinyes, Ares and all other ships ARE visible and work quite normally in-game. They can also be seen quite normally in Ship selection - they just don't appear in Tech Room.
And, EVEN more mysteriously, the Cypher appears as Ulysses in Briefings, when I click below the name... but in-game it appears just as it is supposed to do.
I don't really understand this. Should all these parts of game use the same tables at one time? I don't get it, how the hell can some ship not be available in Tech Room, or to be substituted as Ulysses in Briefings...

However, this is a very minor issue, as everything seems to be working quite fine in-game. Cypher is a capital ship, and all the ships that are missing in tech room are available. It'd just be nice to know what is causing this...