from the about.com web site (http://Golf.about.com/b/2008/01/12/new-cut-rule-victimizes-18-golfers-at-sony-open.htm)
brent kelley explains it this way...
So here's how the new cut rule works: * Low-70 plus ties is still the cutline. If 78 or fewer golfers make the cut, then everything continues as in the past. * However, if 79 or more golfers make the cut, the PGA Tour eliminates additional golfers by going one stroke back from the cutline. If the cutline is 4-over and 83 golfers make the cut, the Tour goes back to 3-over, eliminating golfers at that score. * Those golfers who are eliminated in this extra step are credited with making the cut, but do not continue to the weekend rounds. Since they are credited with a made cut, however, they do get their share of the purse and FedEx Cup points. But there is an exception: If the second reduction takes place and results in a field that is farther away from 70 than the full number of golfers who made the cut, the original number stands. For example, 80 golfers make the cut based on the low-70s plus ties formula. The Tour eliminates all the players one stroke below the cutline, which results in 59 golfers remaining. Fifty-nine is farther from 70 than 80 is, so the original 80 continue to the weekend.
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The cut nearly always takes place at the end of the second round, unless there is a 36 hole and 54 hole cut. If it is a 36 hole cut it will usually take place on the Friday evening, with those players who made the cut advancing to Saturday's round.