Better not get Goob angry...
Anyway, you're not doing it correctly. If you want to play Derelict, you must either move, delete or deactivate FSport. The reason why FSPort 2.3 works with Derelict (actually, it won't, because of the Saphah and the Hydra would become Ulysses fighters) is because FSPort 2.3 is actually compatible with the retail campaign. FSPort 3.0 is not, it lacks most of the weapons and many of the ships that are used in the retail campaign.
So you must remove FSPort before playing any other MOD... It'll take just take a few secs to simply move it or just switch -mod commandlines.
Ehh... Ignore me if you want, I don't want to face anyone's rage, be it yours or Goober's...