Yes! Bloom effect, I couldn't remember what it was called in SHIII. I'm running afew mods (ultimate sound, green lamp button mod) but the problem was there from the start. I manually edited the config for V-sync on and have reset all ATI Catalyst settings to their default - application controlled. As far as the .exe, I have a retail version from Gamestop patched to V1.1 .
I read over at UBI last night that the copy protection may be interfering with certain features of the game like the eyes of the crew. After reading that I fired SH4 up and at certain times the crew have missing eyes

. Kinda reminds me of "Event Horizen" where the crew rips out their eyes. According to the devs, they have found that in afew cases this happens even if running a legit version so their checking into it.
Are you running ATI or Nvidia?