I am having a similar problem - I hate to make my first post requesting noobish help, but unfortunately I'm at my wit's end.
I have a similar setup to badme, most recent CVS build and mediaVPs - I even have them set up just like in the FAQ, in their own directory named mediavps. I downloaded the mission vp, the main FSPort vp, the sparky vp, and even ripped all the voice and cutscene data from my FS1 discs to the data folder of the FSPort directory I made.
Unfortunately, upon selecting the FSPort mod and using multimod to making it load the VPs as well, something is wrong. I can select the FS1 campaign, the ships are working and look good, so obviously the multimod is working fine. What doesn't work is that the main screen is seemingly the one from the FS2. I'm not sure if you guys ever fit in the original's one in hires, but I'll tell ya anyway. My main problem is that upon starting the campaign, I get a Ulysses with no weapons instead of an Apollo as intended. I just did a fresh install and I have no tables in my tables directory to mess stuff up, so I'm pretty clueless at the moment.
Like I said though, the mediavps are working so it doesn't seem to be a problem with the way that I installed said mod, it might have something to do with needing a new table or maybe just some conflict between the latest releases. Any help would be appreciated, and also many thanks for this excellent project's existence.