I am going to go with the theory that it is not 10.6.3 limiting the speed, but you are just now finding out the true speed.
The Hitachi drives Apple use have model names ending in "SAxx", which means they are set to run in SATA 1.5 Gbps mode (source: Hitachi web site, legend for model names). Only if the drives' model names ended in "A3xx" would they be for 3 Gbps mode. That's why those drives are shown as having a negotiated link of 1.5 Gbps; the hardware/firmware of the drive is limited to such.
Also, for the non-Hitachi drives, note that it has been speculated before (and somewhat supported) that Apple has the hard drive manufacturers do a special firmware for the hard drives it uses in the computers for various purposes, and this may include limiting drives to 1.5 Gbps. [Speculation of this was even more well-supported when users of the mid-2009 13" and 15" MBP upgraded to EFI 1.7, and had troubles with new drives running at 3 Gbps but not when those drives were artificially limited to 1.5 Gbps, or when using Apple-shipping drives reported to run at 1.5 Gbps when chucked into another system.] So it is entirely plausible that your drives won't negotiate a link of faster than 1.5 Gbps in any system by firmware restraint at Apple's request.
For the non-Apple drive users where the drive should link at 3 Gbps, please check if it is so on your system. The screenshots so far have been of Apple-shipping drives, and comments about non-Apple drives have not included actual link speed but focused more on the tangible performance during system and program start-up.
I'd hope that a permissions repair, a good Carbon Copy Clone/"defragment" (files can still get scattered across the drive with HFS in OS X, after all, as some failed Bootcamp attempts show), a proper cache cleaning, the standby fix-all SMC/PRAM reset, or a few days' patience applied to this update irons any issues out.