Well, here is what I have tried. I hope you might have a suggestion, I am pretty frustrated with it. Again it is only for PayPal Pro. My customers and I get the emails just fine from PayPal.
I deleted all modifications under system emails, deleted all modifications to any views I had made in my template(yes, I am sure I am in the correct template), switched the hikashop to default css, switched my joomla template to a different template, and changed the checkout workflow back to the default. I have triple checked PayPal Pro settings, even though nothing was changed in between the time it worked and when it did not. Placed an order and still the same.