System Settings Reset After External Drive is Shut Down

I have my System Settings set to have the Autosave Vault, Thumbnail Cache and Waveform Cache live on my external media drive, not my internal boot drive. However, every time I turn off my media drives, the program resets these folders onto my boot drive. It leaves the capture and render file settings alone.
Why is this and how do I make it stop?
Thanks.

It needs to write to autosave vault even if the program is just sitting there open.
If it can't find the specified place to write to, it will go to it's default
Quit FCP befoe you disconnect your drives and start your drives before you launch FCP
Does it let you shut of your drives when it's running? you don't get an error message?

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