I played the FS1 port a while ago using SCP. I also had the Transcend campaign installed. (These were in separate folders using the -mod commandline.) I played the FS1 port mission Where Eagles Dare (I think), and one of the transports went down. My screen flashes black and I'm stuck facing the planet, nothing around me. I can't move my ship at all. This is similar to the scripted events where the Transcendant "captures" you. I fixed it by taking out the Transcend folder from the FS2 directory.
My only question is this: If the campaigns are in separate folders, they can't interfere with each other...right? Unless someone let the Transcendant out of his nebula...
*Horribly garbled transmission*
*Vanishes without a trace*