I'm not using either the Zpack or the music VP, so those aren't an issue. And yes, I do have Karajorma's fix applied. In fact, during the main FS2 campaign, I don't experience any major errors other than the odd crash; it's only with the Port that I've found something this serious.
Karajorma, normally I keep the SCP VP files and the Port VP files in their own separate mod folders. Previous to the most recent VP release, when I wanted to play the Port, I just used the -mod FS1Port flag, since its graphics were on-par with the SCP VP files. However, with the many graphical enhancements added in the latest VP release, I decided to move the SCP VP files to the main FS2 directory, so that any campaign/mod I planned on playing would use the new enhancements. However, when I put the SCP VP files and the main FS2 directory and used -mod FS1Port, that's when I experienced the crashes. It doesn't occur if I set it up the way I always did, with the SCP VP files in their own mod folder. I haven't tried the multiple-mod flag; I'll give that a whirl and let you know if there's any change in what happens.
Edit: I tried the multiple mods flag; the exact same crash occurred. I tested the same mission on which I had first noticed the problem; specifically, "The Darkness and the Light." Interestingly enough, even with the Port folder listed first, the regular SCP splash screen came up instead of the Port's. Is that due to a file type/name change for that particular file?