I have the same issue too. I added a 'Add to cart' button and the add instructions is enabled (this is the default) and there is no area to enter the instructions when you check-out. And I agree this is totally ridiculous not to have this option when you check-out and having the workaround being to add the comment at the front end web site page. The confirmation e-mail even has a section that indicates that the buyer has not entered any instructions!!! And to add insult to the injury they have a feature on the set-up that has been depreciated? It is amazing that 'reputable big' companies like paypal operates like this. This feature to be reinstated as soon as possible!!
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