*** SOLUTION ***
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After days of searching, I think I've found the solution: rollback the Linux kernel.
I have a feeling that the Spectre/Meltdown fix introduced in a recent patch slows down the box enough to cause large file operations consuming a lot of CPU time (like Deluge) to throw errors.
This solution means that your system will be vulnerable to Spectre/Meltdown.
For my setup, the only user software run on the box is deluged, flexget, and openvpn. I'm more concerned about functionality over security. If you install and run different software on your system, this might not be the best solution for you, but as far as I can tell, it is the only solution at this point. Luckily, it's very simple to bounce back and forth between kernels as new ones are released.
I'm running Debian (9.4 Stretch), so this is what I did:
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sudo apt-get install linux-image-4.9.0-3-amd64
At this point, you can simply run:
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sudo update-grub
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sudo vi /etc/default/grub
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GRUB_DEFAULT=saved
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GRUB_SAVEDEFAULT=true
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sudo update-grub
You can always confirm your kernel by running:
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uname -a