I know im late with this post but here I am testing why the hell PS3 stuttering on a brand spanking new hdd.
the new drives are all tested on pc prior plugging it on ps3, passed on all test, specially with hd-sentinel read/write test (destructive test, it will destroy any data on the drive, well its a new drive so it doesnt matter).
the new 1tb seagate mobile drive works fine, but it stutters on some games, like wtf is going on, after some digging on other forums (took me an hour(s) to find a somewhat lead why it was causing this) that is not related on PS3 of some sort. New drives today are now formatted with 4k sectors and this does affect legacy OS such as Windows XP or older, this OS will experience stutter performance. So OK, now I found a lead, I scavenge some old laptops that still have a old Hard drive on it, found a old sata3 500gb hdd that is not 4k (advance formatted hdd) formatted, test it on hd-sentinel before plugging it on ps3, all passed ok. Proceed on PS3 swap drive on a 500GB one and guess what, the issue is immediately gone. No more stutters.
I also tried a another drive which is also 4k formatted drive from western digital, that stutters like hell as well.
so yeah in conclusion. HDD with Advance Fomat (4k sectors) will stutter on PS3. Just look for a old 500GB HDD since most of them are still on 512b sector format, that should work just fine on ps3 without stuttering.
superlateedit:
if you guys want to test if your AF/4k sector drives are stuttering, just iplay beyond two souls digital version, you will see how unplayable it was using the AF/4k sector drives. use a old 500gb drive that is not AF/4k issue is gone.