When looking at the grass, darker shades mean you're looking into the grain, while lighter shades means you're looking down with the grain. Smallville is also correct in that sometimes you can look at the edge of the cup. The ragged side of the cup is the side the grain is growing towards. Every green is affected by grain, just some more so than others. Some tendencies of grain. Grows toward the sun, so it could change from morning to evening. Also grows towards where water drains. Look for drains around the green, or low spots on the course/ water hazards.
Yeah, I'd think it has to do with the grain of the green. I've never played on a course with grained greens, at least not that I knew of. I always wondered how much it affected putts.