A blast from the past, but just in case anyone's still in the same boat...
I've pretty much given up on the idea of Intel or Asus fixing this issue. It only seems to affect a subset of boards, and then only under some circumstances. The main complainants seem to be X52 Pro owners, and since the X52 Pro is now effectively legacy with the advent of the X55 I can't imagine Saitek will be falling over themselves to address it either.
So, annoyed at having lost my USB 3.x functionality I figured the answer might be a third-party USB 3.x PCIe card that used a chipset other than the problematic Intel one.
Long story short, I installed a four-port version of the
Inateck KTU3FR and everything's working perfectly. I've re-enabled xHCI for the built-in USB ports, all of the first- and third-party USB 2.x and 3.x ports are working as expected, the X52 is happily behaving itself plugged into the new card and Windows is stable.
The Inateck card uses the Fresco Logic FL1100 host controller so I would guess that any card using this chipset would probably do the job, although obvious disclaimers apply: I can't guarantee success on anyone else's system, and other cards and chipsets are available.