I "Think" I've found what is causing it, USB 3.0.  Apparently, or at least in my case, the 896mk3 Hybrid "does not play well" with USB 3.0, since all 3 I've had did the same thing.   I had moved to different USB ports, but as it turned it was always another USB 3.0 port. I tried a USB 2.0 port yesterday and today, again, there are no clicks. All the other recording interface units I've had , including Roland Octa-Capture, M-Audio, Tascam, have worked OK with USB 3.0 ports but the 896mk3 Hybrid apparently "doesn't like" USB 3.0 ports. I went back and traced where I was plugging it in, using USB Treeview utility (that shows what is on every USB port) and it was always on USB 3.0 ports, whether an Intel USB 3.0 or Etron USB 3.0 (both are on my motherboard, an ASRock Z77 Professional). It is now on an Intel USB 2.0 port on the motherboard.
 
Maybe MOTU needs to update the firmware?  The date on the firmware is 2012.  Wasn't much USB 3.0 around then. 
 
 

USB 3.0 has not yet become a standard for audio interfaces - even MOTU units of newer design come with USB2 only (and introduce USB 3 only via the thunderbolt options) ...
 
many other units also require USB 2 to work properly - of course, this will become an issue as new computers will eventually only come with USB 3.0

I have/had older USB recording interface units and they all worked OK on USB 3.0.  That included an old M-Audio Ultra 8R that was purchased back in the Vista days when there wasn't any USB 3.0.  USB 3.0 is supposed to be backward compatible with USB 2.0 devices.  I've got many USB devices, all USB 2.0 except one and they all work on 3.0 ports.  The MOTU is the ONLY one that has a (intermittent) problem, and it is ONLY when I use Sonar.  If I use Studio One 3, Ableton, Band in a box, etc it NEVER had the problem, ONLY with Sonar, which is also baffling.
 
The buffers in Sonar are set 512 playback and 256 record, the same as I used with the Roland Octa-Capture, Tascam US16X08 and Steinberg UR44 that I had.

Its all about the drivers, obviously the MOTU drivers don't play well with USB3; at least on your mother board.
IIRC, RME drivers didn't like USB3 when I installed the UFX.
I think they've been updated since, but I put mine on the USB2 and it's stayed there.
Evidently USB3 has no real advantage for audio, or so they say?
DRIVERS, DRIVERS, DRIVERS; kinda like Real Estate, location, location, ah you get it...
T
You got it sussed, that's all that matters!

But, why only with Sonar?

Just for the record, I didn't use a USB 3.0 port to get more speed.  Just what was open and used in the past with other USB 2.0 recording interface units (the original USB 3.0 port I used had been previously used by an M-Audio Fastrack Ultra 8R and then a Roland Octa-Capture and there were no problems).  USB 3.0 is backward compatible with USB 2.0 and when a 2.0 device is attached the USB 3.0 port runs at the USB 2.0 speed. 
I currently have other USB 2.0 devices attached to 3.0 ports and no problems.  It would appear to be an MOTU issue, whether firmware in the device or their drivers. 

My Quad capture would not work on my system using USB 3. I also found out that a couple USB 2 devices were actually USB 1.1 My Cakewalk UA25EX interface was an example.

This is actually a fairly common problem with USB2 audio interfaces.  Yet it seems to plague a lot of users because while they know USB2 and USB3 ports are technically different, they gloss over that fact when it comes time to troubleshoot.
 
Hence, my specificly-worded suggestion a week ago.

That I missed trying a USB 2.0 port early in the troubleshooting is my fault.  The fact still remains, EVERY other USB 2.0 device I have or had has worked perfectly on USB 3.0 ports.  The ONLY device that exhibited a problem is the MOTU 896mk3 Hybrid.  Because everything I've had has worked OK on USB 3.0 there was no reason to suspect the MOTU would not work on USB 3.0 ports.   

fireberd
That I missed trying a USB 2.0 port early in the troubleshooting is my fault.  The fact still remains, EVERY other USB 2.0 device I have or had has worked perfectly on USB 3.0 ports.  The ONLY device that exhibited a problem is the MOTU 896mk3 Hybrid.  Because everything I've had has worked OK on USB 3.0 there was no reason to suspect the MOTU would not work on USB 3.0 ports.   

did you ever raise this issue with the MOTU support?