Mojo in general may not be the problem, but I'm not convinced that my particular unit doesn't have an issue.
I literally have the fastest Macs it is possible to buy today. Other's are having it work fine with MUCH slower hardware with far fewer resources. The ONLY common factor with this issue is the DAC. So either my DAC has an issue or there's something common to my computers that I don't know about (one of them, a fully-specced Retina Mac Book Pro was brand new as of yesterday - so there's no third party software in the way).
I avoid JRiver for a variety of reasons - however I included it in my testing as an attempt to eliminate Audirvana as a possible cause. The issue exists with Roon also, so it's not the playback software. And it's definitely not the performance of the computer.
So, after lots more trouble-shooting, I've eliminated my Mojo as the cause of the issue. It's reproducible on at least one other DSD DAC - though dropouts are more frequent with the Mojo for some reason.
About the only thing left to try is play via Windows and a Mac running a pre-El Capitan build of OS X.
I've used five separate Macs, all MORE than powerful enough to handle the "load" (even on my slowest machine we're talking single digit percentage CPU usage). Half a dozen USB cables including Amazon Basics, Monoprice, Anker, AudioQuest Cinnamon etc. It happens with Audirvana+, Roon, HQPlayer, and JRiver. It's more common on higher bit-rate files (up to quad-rate/DSD256), but still happens at DSD128 - not seen it at DSD64 (1x) yet. It'll play all day at 32/352 or 32/384KHz mode (identical data rate to DSD256) ... but put it in DoP mode and the dropouts begin. It happens with all of my native DSD music files. It happens with Redbook audio up sampled to DSD (so not just native files). It happens with native USB 2.0 and 3.0 ports.
At best I can fathom now is that it's a timing issue with data in DoP format (or DoP is less tolerant of timing issues than simple PCM - even though the container is the same). No idea what is causing the timing glitch. Maybe it's an El Capitan issue.
Won't post on it again in this thread unless I can resolve it. But did want to confirm that it was not down to a fault on my Mojo.