There is a good chance it has to do with the various 'C States' in the Bios (I mean the UEFI)..
EIST (Enhanced Intel Speed Step) combined with Turbo Boost is oriented toward Gamers and Green energy usage; it is fine for most applications, but DAW is a different beast.
Basically, Turbo Boost increases the CPU multiplier whenever the processing load gets high.
EIST, C1, C3, etc, put the CPU into a low power state whenever the CPU load is light. Each via different methods, either reducing the CPU multplier & voltage, or shutting down a core or more, etc. The problem with all this is that Cubase wants to see a steady CPU 'state' and has problems when the multiplier is changing 100's of times a second (literally, with Turbo Boost) and then is throttled down to some low multiplier / energy state when the processing load gets minimal.
You may want to investigate all this and then check your bios settings (I mean UEFI~!:)
Of course your problem may be different altogether, but I just researched and put a similar system together and I noticed the bios defaults were set for gamers and overclockers, with ALL that stuff turned on; the CPU was going up and down like a YO-YO. Using Turbo Boost to get arbitrary high CPU speed (and the C States for cooling down & energy efficiency) is not so good for audio recording. Stability is more important.
Check this: http://www.gearslutz.com/board/music-computers/465221-c1e-c3-c6-eist-speedstep-turbo-boost-core-parking.html
The OP, jschild, is Scott from ADK; they build DAWs for a living, day in and day out, so I'm guessing he knows what he is talking about. To sum up what I am getting at above, here is a quote from that post:
modulations in the system timer (even slight) could create
system stability issues
But that is just part of the issue. Go read that post; plenty of info (and a lot of arguing too
Incidentally, it looks like you have a motherboard with Thunderbolt on it. Are you using the Thunderbolt port right now?
If so, you may want to check the mobo specs real close; I have the Asus Z77 V-Pro w/ Thunderbolt; I got it so I could use thunderbolt later when more devices are availble for it. But I noticed that the Thunderbolt bandwidth is shared with the 2nd PCIe X1, the extra Asmedia Sata 3 ports and the extra Asmedia USB3 ports. There are bandwidth limitations on any chipset; you have to pay a lot of money to avoid all that bandwidth and IRQ sharing (that's why Steinberg recommends HP workstations that cost 3 - 6 grand).
The first thing I did was go into the bios and turn the Thunderbolt off, since I have no need for it now.
The same is true of any other 'embedded' feature you are not using on your motherboard: turn it off!
On the software side of things, the idea used to be about getting as much RAM availble as possible, but now, with 64 bit OS, the focus is more on anything that interferes with getting your DAW to as close to 'real-time' as possible. Anything that takes too many cycles or jams up the system is bad, and no amount of brute force processing power is going to solve that issue, so you need to know what is holding up your OS - literally holding it hostage for just long enough to make a low buffer DAW choke. For that, check out:
dpclat, the Deferred procedure Call checker at http://www.thesycon.de/deu/latency_check.shtml
Or better, http://www.resplendence.com/latencymon
The first one is well known, but the 2nd actually tells you what programs or routines are holding up your system.