I am sorry to hear you are having issues, but also slightly relieved that you are!
I am running a new Haswell i7 3TB fusion iMac with Mavericks. It appears that this configuration of new CPU, Fusion Drive and Mavericks which are causing all the issues.
Let's start at the beginning. I bought an iMac with the last gen Intel CPU 1TB Fusion and Mountain Lion. Running a Motu 828MK3 interface. Spending a pretty penny on this computer you could imagine how ****** off I was when weeks later they announced the new Gen Haswells for sale with better graphics cards.
Apple kindley swapped the computers over increasing my storage to 3TB and doubling my graphics card! Wonderfull! When Mavericks came out I naturally upgraded, especially as the Motu website stated that they had worked with Apple to regarding the interoperability of their hardware to the new Mavericks OS.
Upon upgrading to Mavericks, as soon as the interface is required to process sound through iTunes of Logic, about 1-2 minutes into the sound be played back, a couple of pops are heard in the speakers, followed by a high-pitched "weee' sound, LED lights 3&4 of Analogue out flash on the front and then no sound is heard at all!
Given that The new iMac only started to do this when Mavericks was installed, I would say that this is more of an operating system issue than anything else as all worked well with Mountain Lion running the new iMac CPUs and video cards.
DO NOT LET APPLE FOB US OFF WITH PROPTIONING BLAME TO 3RD POARTY MANUFACTURERS!!!
We all seem to be having the same issues concerning the external audio interfaces and Mavericks. To potentially protect the person at Motu who is assisting me, that person may or may not have given me access to a FTP site which held the proposed Maverick OS drivers as all Motu interface at this point were running previously releeased drivers. I can confirm that if I did have acces to such a file it did not resolve my issue 😉 nudge nudge wink wink.
If there have been some resolves by partitioning the the HDD and installing Mavericks on the HDD and not the SSD I would be under the impression that this is an Operating System issue concerning the SSD, Mavericks and then the 3rd party hardware being attached, so in short, it's not Motu's fault but Apple's!
I would urge everyone to please contact their interface manufacturers so they can pile on the pressure to Apple to fix these issues! We all have some expensive kit rendered null and void because of an OS upgrade! If this is the case then I would also assume that non-Apple hardware like Motu will have foreseable issues as long as Apple do not pull their fingers out, which in turn will probably affect potential interface sales bringing a rise to a law suit under Unfair Competition: some hardware is fine which could be viewed as preferential interoperability over other manufacturers.
For all those who are unable to make a wage due to this, start logging your loses, send Apple a heads up email that you are keeping a log of all losses to which they will be liable for re-imbursement until they fix this issue!
In the meantime, fingers crossed to everyone who has issues, I am into over a month now....