Long story short:
1/ I’ve been through 3 macs this year, my 13” MBP, my 17” MBP and now my 15” rMBP.
2/ In between my 17” and 15” I installed the tonymacx86 USB 3.0 drivers on my 17” machine in order to make the USB 3.0 ExpressCard I bought work with my USB 3.0 devices.
3/ After going through he Tonymacx86 install on my 17", the computer started to recognize the ExpressCard as a native USB 3.0 hub.
4/ It worked.
5/ Later in the summer I bought my 15” rMBP, and did a ‘transfer’ install from the 17” to the 15” in order to keep all my software, apps and files.
6/ Unfortunately, in doing so, the system “carried over” these Tonymacx86 drivers for the internal USB 3.0 hub from the 17” to the 15”.
7/ There appeared to be no problem with Mavericks up to 10.9.
8/ However it appears that after I installed Yosemite, something about Yosemite does not jive with these drivers. Unfortunately, it appears that Yosemite does not automatically install all new device drivers on your mac. I think what’s happening is that Yosemite “thinks” I have an ExpressCard slot installed on my current 15” machine, and is just leaving it alone.
9/ So now I'm stuck with NO working USB 3.0 ports on my 2012 15" rMBP.
10/ So, I think rather that install any new updates from Tonymacx86, I would really just like to install the original Mac OS X Yosemite or Mavericks drivers.
UPDATE - UPDATE
Downloaded appleusbxhci.kext for Yosemite beta build 2, used Kext Utility to install it, and it gave me back both ports - but only as USB 2.0.
So, I did a clean install of Yosemite, which brought back the Generic USB host controller driver.
Ran Kext Utility again, but this time, only to repair permissions, not to install appleusbxhci.kext, restarted and then boom - both ports started working again as USB 3.0!
Checked on a system report and instead of the Generic USB host controller driver, it lists the AppleUSBXHCI driver.
So, it's working. Whew!