After some investigation, I have discovered that this clicking and disconnect only happens when all of the following are true:
- I'm on my Windows 7 desktop (specs below) and not my Windows 10 laptop.
- Factorio is running and in game (the menu system won't cause it, and neither will running various other games and applications on my machine)
- I am using my wireless USB headset, and not my desk speakers.
I have verified the game cache and reinstalled Factorio to no avail. Running LatencyMon reveals that USBPORT.SYS is indeed the highest reported routine execution time, though the application still reports that my system "seems to be suitable for handling real-time audio and other tasks without dropouts."
Desktop specs:
Windows 7 Professional 64-bit
Logitech H800 Wireless Headset (connected via USB, not bluetooth)
UtechSmart Venus USB Mouse
Logitech G510s Gaming Keyboard
Intel Core i7 Broadwell @3.4GHz (no overclocking)
ASUS X99-A II Motherboard
32GB of G.SKILL Ripjaws V Series DDR4 3200 SDRAM
I don't really expect any significant progress on this, since I do believe that it is an issue that is (at worst) caused by something else in my system interacting with Factorio. That said, writing this has helped me collect my thoughts and perhaps it will help someone else out in the future.