I'm making assumptions here, so correct me if I'm wrong.
I own the original Descent FreeSpace and Silent Threat, and I also have the original disc 2 and 3 of FreeSpace 2. Following the instructions in the readme supplied with FSPort, I copied the movie and sound files from the FreeSpace CD's and directory into my FreeSpace2 Directory.
I assume, when playing a video, the game looks for the files in the following order: Game directory, then CD Drive.
Because I copied the FreeSpace 1 Intro into my FreeSpace 2 root directory, everytime I load FreeSpace 2, it plays the FreeSpace 1 Intro.
Is there anyway it can be made so that the FreeSpace 1 intro is only loading when starting FreeSpace open with the FSPort mod? Placing the intro into the FSPort folder and having the port look for the file there? Luckily, the end game sequences for the two games are named differently.