The precincts that are heavy for Cobb and Harris also have pretty heavy voting for Badnarik, Nader, and Peroutka. The falloff in voting between the Presidential and Congressional election in Cary Town Hall is over 20%, and in Anguilla Town hall it is over 15%. But in Roaring Fork 3rd, the total dropoff is not that much, but Thompson ran way ahead of Kerry.
So I would suspect some double voting in the presidential race, with a possiblity that a different correction was applied for different precincts. In some precincts, ballots for Kerry and another candidate were counted twice (resulting in little difference between Kerry and Thompson) but a big difference between presidential and congressional totals. While in other precincts, the presidential vote was counted for the minor party candidate. This resulted in similar number of votes cast in the two races, but a big loss for Kerry vs. Thompson.