my 2 cents...
i agree on keeping everything up to date in a theoretical ideal best case scenario..... and i also think that trouble shooting email can be a royal pain....
that said, if the customer gets the email, and the store owner does not, i can only think of the following scenarios:
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it strikes me that something is wrong in the configuration; specifically the email address that copy of orders go to: SEND_EXTRA_ORDER_EMAILS_TO
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OR the email is getting sent to the store owner and the store owner is not receiving it...... the blocking and/or filtering of various email servers can be difficult to troubleshoot.
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OR the store owner is getting it and his email client is doing something with it, ie putting it into another folder, marking it as spam, etc so that the store owner can not find it.
there are a multitude of reasons why the store owner is not getting the email; but if the customer is getting the email, i find it hard to imagine that upgrading with solve this problem. i could be wrong.
one last thing, if you are using a free email service to send the email, i would look to see if it is receiving the send email message. if the customer gets the email, there should be a record of it at the free email service (at least there was one when i played around with a free email service); you can then see if the email to the store owner is there as well. if it is not, then you know you have a problem with ZC. i hope that makes sense.
good luck!