This item is from the Yet Another Enhanced IDE/Fast-ATA/ATA-2 FAQ, by John Wehman and Peter den Haan with numerous contributions by others. (v1.92).
Believe it or not, but this is completely normal. First, filesystem fragmentation affects some benchmarks; try defragging the drive. Second, not all parts of the drive are equally fast.
Physically, a harddrive consists of one or more rotating platters, where the tracks are concentrical circles on these platters. Obviously, the outermost tracks are longer than the innermost ones. Because they are longer, they can hold more sectors. As you work your way inwards and the track length decreases, the number of sectors decreases in a number of steps. This is referred to as Zone Bit Recording (ZBR).
Back to the benchmarks. Since the platter spins at a constant rate, more sectors in a track give a proportionally higher transfer rate. The very first cylinder of your drive is right at the edge of the platter, in the fastest zone. This is the area that was tested when you got your drive and tried to find out how well it performed. As your drive fills up, you start using higher cylinder numbers---and slower zones. Depending on the type of benchmark you use, this may be reflected in lower scores.
The difference in sectors per track (and hence transfer rate) between the fastest and the slowest zone may be as much as a factor two. Typical drives have anything from five to twenty zones, all with a different number of sectors per track.