From what I have gathered it sounds like the controller and the stock hard drives are both limited by firmware to 1.5, but with the 1.7 firmware you can open up the controller to 3.0.
Then if you add a hard drive that is not limited to 1.5 Gb/s you may or may not have problems. Some people are able to run with both the controller and hard drive (or ssd) at 3.0 and some are not, and have to put back in the 1.5 Gb/s stock drive. Some other people seem to be ok when they limit the 3rd party drives to 1.5 with either a jumper or 3rd party hard drive firmware.
My guess is that it could be a problem or variance in the controller chips that made Apple limit all of them to 1.5 for stability. Kind of like when you overclock a CPU and some can handle it and some can't.
So if that is true Apple kind of sidestepped the issue instead of totally fixing it, and that may be why they specifically said that they won't support the 3rd party drives, because they are all running at 3.0, which makes some of the controllers puke.
That is my theory of what is going on.
Hopefully it can be fully fixed because I was planning on getting a new macbook pro and ssd.