I was wondering which option in the menu controls the visual effects? I've only really noticed it in space, but a lot of visual effects fade in and out of existence for me. For example, pretty much every time Gravity Well is used, it appears on my screen for a few seconds, then I no longer see it for a few seconds, then it comes back again. Other abilities do the same thing: Eject Warp Plasma, Vent Theta Radiation, Power Siphon, and more. I also noticed this happens a lot with ship debris, particularly Borg Transformers and Gates in STFs.
The abilities, themselves, always appear to have their active effects, it's just half the time I can't see them. This is particularly irksome when I'm gaming with a friend whose loadout compliments mine, and I use an ability while his is still in effect since it looks like it ended. My friend also has the same issue in regard to phasing visual effects.
My computer is pretty top of the line, and the game runs flawlessly other than this visual glitch. All settings are set to high with the exception of Bloom, which is set to low. If it helps, here are my specs:
Intel i5-2500k @4.2Ghz, 16 GB 1600 RAM, GTX580Ti, Vista 64-bit.