These effects haven't changed in years. If this is just now coming up, I suspect engine changes or video card driver issues.
My (admittedly uneducated) suspicion is that it's engine changes. I've got two completely different machines that experience basically the same problem with completely different video cards (one's a crappy laptop that can barely run Freespace 2 Open, the other is gaming PC that runs it just fine).
Most likely changes haves been made to how postprocessing works that has somehow become incompatible with the FSPort MediaVPS
I haven't noticed any issues the Freespace 2 MediaVPS using postprocessing, only the FSPort ones.
It would help if more people tested it to confirm though - it's easy enough to test. Install F2, use Knossos to install MediaVPS, FSPort and FSPort Media VPS, set FSO Options>Graphics to include Post Processing. Start a new game and test by shooting the ML16 in the first training mission.
Compare to how it looks with post processing turned off.
Assuming this is a problem introduced through engine upgrades, is there any way for me to report it to someone who might be able to look into it and fix it?