http://www.chess.com/tournaments/help.html#groupings
The official explanation applies only when all groups are full.
The actual explanation that applies in all situations: "For multi-group tournaments, players are placed into groups starting with the lowest rated player, in the last group, sequentially up to the highest rated player. For example, in a 25-player tournament with 5 groups and 5 players in each group, the lowest rated player goes into Group #5, 2nd lowest rated player into Group #4, 3rd lowest rated player into Group #3, and so on. After all groups have one player, it starts all over again at Group #5. So, in this example Group #1 would have the following seeds: #1, #6, #11, #16, and #21. This is done to try and ensure that in the final round, the best players will be left playing for the tournament win."
in open tournaments are higher rated players seeded so as not to play each other if so you should advertise the fact when asking players to enter these tournaments either way i do not think fair to favour the higher rated players what does other lower rated players think not just the higher rated players as they are biased