Issue: Error Installing

You have not uploaded all of the files in 4.0.1. I would recommend downloading the ZIP again. It sounds like you "downloaded a patch, containing only files changed since" a version that you didn't actually have installed.

It's a completely new installation, I downloaded the package again to be sure, it's not an upgrade package. The file exists as well, and has contents inside it. I had 4.0.0 RC 4 installed before that, but it was removed (VaultWiki removed, then VaultWiki Routes, then files deleted).

BTW, now when I hit Members it says:
Robust, you do not have permission to access this page. This could be due to one of several reasons:

Your user account may not have sufficient privileges to access this page. Are you trying to edit someone else's post, access administrative features or some other privileged system?
If you are trying to post, the administrator may have disabled your account, or it may be awaiting activation.

If the word "patch" is in the ZIP's filename followed by what looks like a date, then it's not the full package. The issue you quoted (vw_Cache_Model::queue_update error) in your first post has been reported before and was always due to an upgrade package being used over an old installation that didn't match the selected package. However, if the correct file is uploaded and contains queue_update as expected, then the error can also be due to a stale PHP opcache which would need to be reset by you.

The Members area was disabled temporarily while we issued security patches: https://www.vaultwiki.org/articles/168/

It's the full package I have installed. The file it's looking for exists, but I don't think the method does.

Restarting php5-fpm fixed it. Thanks.