I can see a lot of people that use wireless keyboards and mice have problems. I use wired ones.
I have the same D54250WYK and use W 8.1 Pro (earlier W7). And I have 5 HDD’s in USB 2.0 boxes and 3 SSD’s in USB 3.0 boxes. All the boxes are from Sandberg. I always use the latest drivers and BIOS.
There have never been problems playing videos from the boxes with VLC or WMP.
There was a problem with one of the Chinese USB 3.0 cables that came with one of the boxes; it didn’t fit properly in the USB Mini Slot so only 40 Mbs could be written to the drive.
I have exactly the same problem. I run a torrent client and I see this error that files and folders have dissapeared, yet upon recheck everything is in place. Though it's very random - sometimes occurs a few times per day, sometimes don't see it for a few days.
Windows 7 + WD My Passport (external USB3 drive)
In my case, with an USB 3.0 stick 'Patriot' 64 Gb, video playback cuts suddenly, some of the menu options of the right mouse button, for example 'delete' disappears, and the only solution is to uninstall the driver USB 3.0 and install the Windows USB 2.0 driver. It's a shame that Intel does not know how to fix this problem.