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When sharing folders in VirtualBox, what is the difference between checking "Make Permanent" and "Auto-Mount", my guess is the second one mounts it once the window closes, and the former one mounts it every time the virtual machine boots. Is this correct?

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The "Auto-Mount" will be executed first after reboot of guest OS while the "Make Permanent" shall share folders in a running guest OS.

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    This answer is confusing. First, you answer "Yes", then what you write afterwards is the complete opposite of what is written in the question. Which one is it? – HelloGoodbye Nov 21 '16 at 12:59
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    Yeah, this answer is pretty cryptic. – Teemu Leisti Feb 5 at 9:01
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When adding a shared folder on a running VM, "Auto-mount" will mount the folder immediately but the mount will not stick after reboot. "Make Permanent" makes automount VirtualBox shared folder persistent (sticks on reboot).

I usually check them both if I wish a shared folder to be always available.

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The VBoxManage manual offers very clear descriptions:

transient AKA not permanent:

Specifies that the share is 'transient', meaning that it can be added and removed at runtime and does not persist after the VM has stopped.

The description is a little confusing. What it means: Transient shared folder cannot be added when the VM isn’t running. That’s because they expire when a VM is stopped, so adding transient shared folders when stopped is meaningless.

automount:

Specifies that the share will be automatically mounted. On Linux distros, this will be to either /media/USER/sf_ or /media/sf_ - depending on your guest OS. Where is the share name.

On Windows, a mounted shared folder will appear as a mapped network drive. It can still be accessed when not mapped, just like a file share.

On Linux, I’m not aware of a way to access the shared folder without mounting it.

On Linux, automounting is only done once during startup. IIRC that’s not the case on Windows though.

While inconvenient, you can indeed have a shared folder that does not mount automatically but is permanent nonetheless.

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    I find your words ironic: "The VBoxManage manual offers very clear descriptions:"..."The description is a little confusing". Seems a little contradictory don't you think? :) – Gabriel Staples Sep 20 '18 at 22:01

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