In the past I've been vocal (on a rant) about my 896Mk3 Hybrid not working with a USB 3.0 Port (get dropouts).  The motherboard I had at the time, a Z77 had both USB 2.0 and an Intel USB 3.0 controller.  Others (including reports on the gearslutz forum) have also reported USB 3.0 issues with some other MOTU units.  I built a new DAW Desktop that only has USB 3.0 and 3.1 ports on the rear I/O panel.  Because of that I installed a PCIe Firewire card (with T.I. Chipset) and have been using that with the MOTU.  
 
I came across a post on a forum of a user that was using 3.0 with their 896Mk3 Hybrid and apparently no problems.  On a whim I connected mine to a 3.0 port on the new PC (a Z170 motherboard with Intel USB 3.0 controller) and surprise it worked OK and no dropouts just playing back some recorded sessions.  I had a song demo session this morning (laid down 3 demo songs) and the MOTU worked perfectly for the recordings, no dropouts!
 
Only thing I can think of is the Intel USB 3.0 port on the new motherboard is a later version.  There hasn't been any driver/firmware updates from MOTU.
 
Jack