Getting blank regions in my SDI audio capture

I'm using an UltraStudio SDI USB 3.0 capture dongle and am capturing 2 channel audio, 48Khz, and the source on the other end of the SDI chain is sending analog audio through the pipe. On the receiving end, if I look at the captured audio waveform, I'm seeing sections where the smooth 16 bit waveform is interrupted with chunks where the audio waveform is set to 0. It's causing distortion in the signal, sounds like crap, etc. I would have thought this wasn't possible... SDI is capturing the audio with it's own genlocked 48Khz clock (I assume) and transmitting this across the SDI cable into the UltraStudio box, I should be getting a smooth waveform back, with no buffer overlaps or time dropouts. And get I'm getting chunks of cut-out audio. Any idea why? See attached JPG of save-to-uncompressed AVI...

Have you tried capturing video as well to check that you're not getting drop out on the USB 3?
What motherboard/USB 3 controller are you using with what driver, and what version of the BM drivers are you using?