If it were me, I'd avoid using El Capitan for any application that requires stable USB connections through an external USB hub.
A partial explanation (and even fix! but only for Intel USB controllers) can be found here, but be warned, it's a pretty deep flaw whose explanation is complex:
https://github.com/RehabMan/OS-X-USB-Inject-All
If you want the more comprehensive and rather complex reason USB 3.0 and external hubs don't work well in El Capitan, the best explanation I can find is of course on a Hackintosh board:
http://www.tonymacx86.com/threads/guide-10-11-usb-changes-and-solutions.173616/
Long story short, someone who really didn't know how to properly program for USB devices programmed the USB stack in El Capitan, and they had to hire another guy to fix it, but the fix was even more of a ****** hack that renders most USB 3.0 external hubs as useless garbage except for certain chipsets, and only 4-port hubs or smaller can be expected to work reliably.
Sonnet probably knows about this situation and rather than make users jump through hoops or complicate things, they probably (and properly) just choose not to support El Capitan (10.11) for their USB 3.1 card.
tl;dr: Don't trust El Capitan's USB stack for USB 3.0 external hubs
A partial explanation (and even fix! but only for Intel USB controllers) can be found here, but be warned, it's a pretty deep flaw whose explanation is complex:
https://github.com/RehabMan/OS-X-USB-Inject-All
If you want the more comprehensive and rather complex reason USB 3.0 and external hubs don't work well in El Capitan, the best explanation I can find is of course on a Hackintosh board:
http://www.tonymacx86.com/threads/guide-10-11-usb-changes-and-solutions.173616/
Long story short, someone who really didn't know how to properly program for USB devices programmed the USB stack in El Capitan, and they had to hire another guy to fix it, but the fix was even more of a ****** hack that renders most USB 3.0 external hubs as useless garbage except for certain chipsets, and only 4-port hubs or smaller can be expected to work reliably.
Sonnet probably knows about this situation and rather than make users jump through hoops or complicate things, they probably (and properly) just choose not to support El Capitan (10.11) for their USB 3.1 card.
tl;dr: Don't trust El Capitan's USB stack for USB 3.0 external hubs
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