Dunno. SFC3 is quite picky.
Try downloading Chris Jones' TNG Mega Mod. It adds like 30-40 new ships to the game (brand-new models, complete specs) including a Sovereign with quantums and type-11 phasers, and a Defiant-class with pulse phasers and quantums, and even the USS Defiant with a cloaking device. Not to mention an assimilated defiant and voyager...
And it even comes with batch files! Double click on Orig.bat and it puts in the standard specs, so you can play with unmodded people. Double click on TNGMega.bat and it puts in the mod specs so you can play on your own or with other modded people. I'm even hosting a dynaverse server for the mod (requires the patch, the mod, and all the mod's updates)