Okay, sorry for leaving this thread hanging. I've got an update.
So it's not just FS Port and a few older mods anymore, not it's mods that worked fine beforehand. In particular, War In Heaven, though AoA is an example as well.
As for the "Disable Setting of Gamma": I tried it, and it worked...sort of. It locked my gamma/brightness at a specific level, and it didn't change. The problem, however, is that that unchangeable level is still way too dark. There are many times where I can barely see a corvette that's right in front of me.
So I turned it off, and the issue is still everpresent. It's bordering on making the game unplayable, and it's rapidly pushing me to the end of my patience.
However, there is something that I'm not sure I mentioned before, that might help. Basically, those "blackouts" I described above still occur relatively frequently (1-5 times per mission, roughly) , even though nothing changes due to the Disable Setting of Gamma being checked. I wonder if there's some kind of monitor refresh rate issue, or something, going on. Additionally, when enabling cheats, my game tends to lock up for several seconds before resuming (with cheats now enabled, though). It might be related somehow, but I have no idea.
Any help would be greatly appreciated.
EDIT: Some additional info: this problem occurs (with the same frequency and degree) on both my external, VGA-connected monitor and on my laptop's screen. Difference in resolutions doesn't change it, either. My drivers are up to date. My monitor's (and laptop's) refresh rate was increased to see if it made a difference, and it did not.