I bought a caddy for my internal HDD as I had this issue too. I have to keep unplugging and plugging the caddy back into the USB when I first start my box every morning. I think the box isn't supplying enough power, even though the light for the caddy comes on straight away if I forget to unplug and plug in first... Irrigardless I'm still happy with my box. It recognises my own powered HDD all the time, that's my main one.
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Sent from my Nexus 6P using Tapatalk