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Auto-update metadata is found in the Send to Device preference in calibre. In the Metadata management box, check that you have Automatic Management checked.
In the Store or Restore Bookmark item, I's suggest not selecting the Set data to now button.
As for your error message, you seem to have a profile Steve set in the Kobo Utilities customization which does not have the #percentread column defined. Personally, I use the default profile for all devices.
I've attached a few images of what my setup looks like.
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