I have exactly the same problem. Most often during cutscenes (especially any conversation with the Elusive Man), but sometimes in certain areas while moving around (In the trial chamber at the migrant fleet is terrible). Once something triggers it, it seems to persist even after leaving the area that started it.
Every second or so I either get a black frame or the frame will appear to "jump" down around 4 inches on the screen. When this happens the game also pauses for around 100 milliseconds or so.
I find that alt-tabbing seems to sometimes clear it up for a little while, as though some thing is being "reset", but it doesn't last if I am in area that seems to cause it.
Turning off graphics options doesn't seem to make it better.
I have never had any problems with any other game, including Dragon Age, which has always performed flawlessly.
I am at work, so I don't have all the details of my machine. This is what I can remember off of the top of my head:
Intel Core 2 Duo 6600.
ATI Radeon 4870X2
4G of memory
Playing at 1920x1200.