Perhaps you should check your drive model in System Information - Storage - Media Name:. You may not have this particular 3Gbps drive in your computer. I wonder if that 5400 rpm drive can exceed the 1.5 Gbp/s that your system is reporting?
My OEM Fusion Drive (FD) components show two different negotiated speeds that are apparently based on the storage media limitations. This SSD negotiated the 6 Gbp/s rate while the HDD only managed a 3 Gbp/s rate.
My other MM 3,1 late 2009 (I removed the opti for a HD carrier) has link and negotiated 3g SSD and 3g 750GB (Apple) drive (originally this drive was from another machine).
My other MM 3,1 late 2009 (I removed the opti for a HD carrier) has link and negotiated 3g SSD and 3g 750GB (Apple) drive (originally this drive was from another machine).
Those drives aren't exceeding 1.5Gb in transfer rates- they're likely under 1Gbps at maximum, so in this case there's no performance penalty. The drives probably are SATA 1, but as mentioned before this post, you can search by the disk's model number to find specifications.
Yup, even the fastest 2.5" mechanical drives won't saturate the slowest SATA link so it's nothing to worry about.
SSDs are a different story - the Nvidia MCP79 chipset in these machines is a bit picky about link speeds therefore most current SATA 6Gbps SSDs won't sync above 1.5Gbps.