It could be the drive advertises a combination of properties – like NCQ, FUA, 1.5G/3G link speed etc. – that results in most current SATA drivers choosing a subset that the drive itself supports poorly. I'd be particularly suspicious of the power management options, because servers (where these kinds of drives were mostly used) typically mostly ignore those, but desktop machines tend to try to implement. Basically, I suspect the actual firmware on the drives is older, and advertises features that weren't commonly used at the time (on servers at least), but now are, but severely degrade the drive performance.
In Linux, I'd look at what properties/parameters your SATA chipset driver provides, and check if overriding (downgrading some of) them yields better performance. If you have both ACPI and libata drivers for your chipset or USB adapter, I'd also check if switching between the two yields a difference in performance.