"When I've had problems like you describe, it turned out to be the tuner - either low reception, overheating, some conflict with the motherboard, or a bad power supply on my HDhomerun. It's easy to rule out the hard disks so do that first"
I tend to agree now that the OP has seen the issue on live TV. I originally had purchased the Duet tuner also, because it was it was cheap, and I'm cheap. I ignored all the bad reviews it got about randomly vanishing from device manager thinking "it won't happen to me"' Well, it did. so instead of wasting my time trying to save 30 bucks I bought the Hauppauge 2250 and have had zero problems since then. But in my browsing for a solution before that I found a post that indicated a PCIe bus problem as far as voltage levels went. That indicated to me a fundamentally bad design.