There is the issue of cluster size in the formatting of the hdd. For a given cluster size setting (usually not something you get to set, but rather a consequence of the default disk format that is used), a larger harddrive will have to give up more space just for addressing.
Think about the days of FAT16. It uses a relatively small cluster size to index the total space on the disk. This was fine when hdd's where in the sub-1 GB range. However, you start to lose considerable capacity to the formatting as you go past 1 GB in disk size. So then came along FAT32 which used a larger cluster size to index a larger hdd. This was fine back in the days of 10 GB hdd's, and even served well in the 10's of GB size range. However, things are probably getting long in the tooth again now that we are past 100 GB's and closing on the TB range. So that is probably what is happening in your 250 GB hdd. The cluster size of the formatting is taking it's "10%" out of the total capacity, which on a 250 GB drive turns out to be a considerable amount of space that you will never get to use. It's probably not FAT32 in your ps3 hdd, but I'm guessing it is something that adapts the same cluster size as FAT32.
I need your sweet love, Rosetta Stone girl!