Jumping in on this thread. I have some interesting data. I'll be as concise as possible...
I just received my new (late 2013) Macbook Pro 15" Retina 2.6 i7, 1TB flash, full-spec, $3299.
Using Behringer U-Phoria UMC204 96kHz interface
Interface worked well on my mid-2009 MBP, which I was finally upgrading.
As you probably expected, falls on its face with the new MBPr (on either USB port)
Connects and is recognized immediately as a Behringer UMC204 by the system.
Output test with iTunes: plays crackle-noise for a few seconds and then goes silent.
Output via Safari, YouTube video: plays crackle-noise for a few seconds and then goes silent.
Connection test with Garage Band: Gets dropped after a few seconds with message "no longer available".
No change with powered USB hub.
No change with passive USB hub.
Also of note: About this Mac/More Info/System Report/Audio gives this message:
"There was an error while gathering this information."
Spoke with Apple Care, level 1 rep (friendly but clueless) and supervisor (friendly but unable to help).
Told to take entire setup in to local Genius bar and test against other new machines for possible hardware problem with my specific machine.
I did so today.
Interface failure on 15" MBPr 2.0
Interface failure on 15" MBPr 2.3
There was no 2.6 unit in stock for me to test.
Neither of the in-store machines had the error message I get in my System Report, but behaved identically to mine.
We decided to test an in-store Apogee ONE interface.
==> Worked immediately on all machines tested! <==
Very interesting.
This doesn't help me (or any other audio pro) but it does cause me to question what Apogee is doing with firmware or architecture or whatever that other manufacturers are unaware of.
Obviously, my issue is not with a Fusion drive.
(I use a Seagate hybrid in my 2009 MBP, and new model is 100% Flash)
I don't know if my issue is with USB3, or Haswell/Crystalwell, or both.
Nobody else seems to know either.
Maybe Apogee engineers know.
Hopefully Apple will know soon, and from this thread it sounds like 10.9.2 could be the answer.
The Genius is escalating my case to Apple's engineering department.
One final comment for the few people in this thread who feel as though they have not been heard by Apple:
Clearly, this is a major headache that has cost us time, money and trust.
In my business, I wouldn't be able to sleep if I sold my customers something that performed as horrifically as this.
But I must say that everyone I spoke with at Apple seemed to take this problem very seriously, and while not acutely aware of the ins-and-outs of pro audio (no pun intended) I did not detect any diminishment or invalidation of my problem as a "minority" or "boutique" issue.
After all, Apple sells Logic and includes Garage Band with every Mac.
They also want their stock to go up.
And we tend to spend money.