I don't think Lee has an extra gear on the field. He's not some kind of a burner. He had a long catch-and-run against Arizona in 2012 where he caught the ball in stride with about a yard of separation between him and the chasing defender. He proceeded to take it about 50 yards to the house, but during that time the gap between him and the DB didn't really grow it all. He was juuust fast enough to stay out of reach. When you see a real sprinter like Thomas Tyner or Ted Ginn get into space, forget about it. Once they hit their stride they pull away from everyone on the field. I don't think Lee is like that.
I think there are a few things at work though. 40 times are run out of a track stance. Receivers come off the line in a much different stance. So if you have someone with legitimate speed, but horrible starting technique out of a track stance, it's going to kill his time in the 40. I think that probably explains how guys like Chad Johnson and Bernard Berrian could run pedestrian 40 times and then consistently burn people deep on the football field. Chad Johnson averaged something like 21 yards per catch in his one season at Oregon State. I think he ran something like a 4.61 at the combine. That time doesn't make any sense and isn't an accurate reflection of his game speed. Another example would be Andre Ellington last year. His time was a total lie.
The other issue is that 40 times measure 40 yard speed, whereas football is really played in smaller windows. You're not going to run a lot of 40 yard routes in a football game. If you're a wide receiver, a lot of the work you do will be within the first 10-15 yards of the LOS. That means that acceleration and quickness are a lot more important than flat out speed. It's more about how quickly you get up to a decent speed than it is about being the fastest guy on the field. I think that's why a guy like Keenan Allen can be successful despite having a slow top speed. He accelerates quickly and has good quickness/fluidity in his routes.
Finally, it's important to remember that there aren't as many elite sprinters out there as we sometimes think. If you run a 4.50, you're going to be faster than almost every linebacker you'll ever face. You'll be faster than a lot of safeties and even a fair amount of corners. In any given week, there may only be 2-3 guys on the other side of the ball who can catch you in a dead sprint. So if you get a little bit of space, you're still going to be break a lot of big plays.