Hello!
I have the same problem with my macs . Both runs MacOS 10.9.5 Mavericks.
I have SanDisk Plus 120Gb in Mac Mini (early 2009) and SanDisk z400s 128Gb in Mac Mini (late 2009).
In "early 2009" SanDisk works sometimes 3Gbit, sometimes it goes to 1,5Gbit. I cannot understand what affect at behavior like that. If I boot from external (over USB) HDD, I got 3Gbit/s every time! At this time no solution for this Mac.
In "late 2009" I had the same problem. Because I do not need DVD, I removed DVD from top bay and put Optibay (cheap from China) at that place. Then I installed SSD at lower bay and moved old HDD in Optibay. I clone HDD to SSD and made SSD as boot disk. There was no success - each time after I reboot I accidentally got 3Gbit/s or 1,5Gbit/s, for no reason. Again, if I boot from external HDD, I got 3Gbit/s! At last, I swapped HDD and SSD. I put HDD back in lower bay and SSD in Optibay. Well, in this configuration I got 3Gbit/s more times, bot not each time. Then I noticed a small switch in my Optibay. After I put the switch in another position, I got 3Gbit/s every time I boot or reboot. So this solves the problem.