Open the ship plugin (in scripts/Custom/Ships) and change the Foundation.ShipDef( part to Foundation.FedShipDef(
Be sure to not change the part before the =, or after the (.
You didn't provide a link to the mod (and I don't have the time to track it down) so I can't give you more specific details.
To give you a reason as to why this happens, the original author didn't specific the "race" correctly (Federation, Klingon, Romulan, Borg, etc, etc) so BC assigned it the "default" race. And NanoFXv2Beta gave it it's own sound.