Hi, as you perhaps know the group of sectors of the Advanced Format drives has 4*512 byes therein. This is, four sectors have been packed into one group of sectors. Therefore the drive gives its best performance if each cluster coincides with the big sector. Your computer still sees it as made of 4 independent sectors, but these sectors are not independent, they are read and written all four at the same time. So, if the cluster does not match this group of 4 sectors, and you have 1 sector in a cluster and 3 sectors in the next cluster, or 2 sectors in a cluster and 2 sectors in the next cluster, or 3 sectors in a cluster and 1 sector in the next cluster, your drive will have to read/write 2 groups of 4 sectors for each read/written cluster. This makes it very slow, and this is the cause of many reports that the drive is severely underperforming.
Happily, there is a solution for this problem: for FAT32 and NTFS partitions there is the program WD Align, I reccomend using the boot CD (powered by Acronis), since it does not require an installed operating system and therefore it is able to access all partitions, some of which would otherwise be in use. WD Align takes care that each cluster has 4 sectors and that each cluster corresponds to a pack of 4 sectors.
What about Linux? Here is a tip: Make a FAT32 partition (quick formatted), align it with WD Align (it takes at most a couple of minutes to do its job, since the partition is empty). Then format the aligned FAT32 partition with mkfs.ext4 /dev/sd… (or mkfs.whatever /dev/sd…). Then install Linux on that partition and it will work at full speed.