Mysterious folders keep generating on their own

Possible Fixes for El Capitan or Later

You should try each, one at a time, then test to see if the problem is fixed before going on to the next.

Be sure to backup your files before proceeding if possible.

1. Resetting your Mac’s PRAM and NVRAM
2. Reset the System Management Controller (SMC)
3. Start the computer in Safe Mode, then restart normally. This is slower than a standard startup.
4. Repair the disk by booting the from the Recovery HD. Immediately after the chime hold down the Command and R keys until the Utility Menu appears. Choose Disk Utility and click on the Continue button. Select the indented (usually, Macintosh HD) volumeentry from the side list. Click on the First Aid button in the toolbar. Wait for the Done button to appear. Quit Disk Utility and returnto the Utility Menu. Restart the computer from the Apple Menu.
5. Create a New User Account Open Users & Groups preferences. Click on the lock icon and enter your Admin password when prompted. On the left under Current User click on the Add [+] button below Login Options. Setup a new Admin user account. Upon completion log out of your current account then log into the new account. If your problems cease, then consider switching to the new account and transferring your files to it - Transferring files from one User Account to another.
6. Install Combo Updater Download OS X El Capitan 10.11.6 Combo Update or Download macOS Sierra 10.12.5 Combo Update and install.
7. Reinstall OS X by booting from the Recovery HD using the Command and R keys. When the Utility Menu appears select Reinstall OS X then click on the Continue button.
8. Erase and Install OS X Restart the computer. Immediately after the chime hold down the CommandandRkeys until the Apple logo appears. When the Utility Menu appears:

1. Select Disk Utility from the Utility Menu and click on Continue button.
2. When Disk Utility loads select the drive (out-dented entry) from the Device list.
3. Click on the Erase icon in Disk Utility's toolbar. A panel will drop down.
4. Set the Format type to Mac OS Extended (Journaled.)
5. Click on the Apply button, then wait for the Done button to activate and click on it.
6. Quit Disk Utility and return to the Utility Menu.
7. Select Reinstall OS X and click on the Continue button.

I have all my apps and OS on an SSD with aliases to the home folders on my fusion drive.

That's an odd setup, can you explain? Do you have two SSD's installed with a spinning hard drive.

A Fusion drive contains an SSD and a spinning hard drive. The OS automatically places apps and hot files onto the SSD portion and other files onto the spinning portion.

Do you split your Fusion drive into separate components?

Aliases rarely ever work for what you are attempting to do. Symlinks are better, but not the best solution. Not sure if it is causing your problems, though.

Some libraries like iTunes and Photos can be pointed to a different drive.

For other stuff, moving the home folder is the best solution as long as the drives are both internal. It will work off an external, but you may run into a point when the external isn't ready when the user logs in. It is less common with an internal.

As mentioned, your rather odd setup may be causing the issue as whatever app is trying to write its data files cannot actually find them through the aliases.

If you can see both the SSD and HDD, then you don't have a Fusion drive anymore. You just have two drives you are using independently. Hence my confusion as to how you were designating where you put things.

I don't think I can figure anything out from the logs.

Are you using some sort of Virtual Machine running Windows? I don't know of any Mac programs that would create that, but I'm sure I've never used every one of them. It does get a lot of hits for Windows.

According to that screenshot, you are using an extefnalbSSD For your data. Without some further explanation I have no idea what you are doing

So you boot from an external drive?

Despite it being an SSD, that would be slower than booting from the Fusion drive.