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This is almost certainly an issue with the middeman: the credit card processor. If the card is getting authorized that means it's working at the merchant level (in this case the restaurant) and you seeing the authorization means that it's working on the card issuer level. Most likely what is happening is that when the merchant's card processor sends back the tokenization to the CC terminal, it was sending an invalid token due to either a setup error or that combination not being properly certified. Most likely, this has been a widespread issue with specific combinations of that card, hardware, and the card processor. Glad they identified the issue and were proactive about giving you something for your trouble!
It's not really a security issue as the PIN on the chip is encrypted. Usually you can still change them at ATMs or in a branch, you just can't do it online or over the phone as there is no way to access the chip via those methods. It's mainly a benefit of off-line terminals which are not common in the US but more numerous overseas.
This is the chip card reader I bought:
https://www.amazon.com/gp/product/B00PY0CNYM/ref=oh_aui_detailpage_o05_s00?ie=UTF8&psc=1