When I do a large file transfer from my external USB3 hard drive to my internal hard drive (or vice versa), be it via Nautilus or via terminal, Ubuntu (Unity) will almost completely lock up. Things like alt-tab take 20 seconds or more to complete while the file transfer is running. This is not the case when there are lots of random reads/writes to the disk, such as when installing packages.

When I was running Windows, I could run a file transfer in the background and still be able to do things, albeit more slowly when something needed to access the disk. I could still alt-tab just fine.

It seems that Ubuntu prioritizes the file transfer above all other disk I/O, which is why it locks up. In Windows it appears that file transfers have a lower priority, which means the system can stay responsive while the disk is saturated.

How can I fix this? It's rather annoying, as the computer becomes completely unusable when copying files. This issue happens in both 14.04 and 15.10. I'm forced to plug my hard drive into a USB2 port to prevent this issue, and that results in much longer transfer times.