Magento 2 – New Orders Not Showing in Orders Grid but Payment Received

When Check/MO method is used, the invoice is created post checkout once you've received funds for an order. There is a checkbox letting you decide whether or not to send the invoice emails when you create these invoices.

When the PayPal method is used and configured to use the "Sale" mode, these invoices are created at the same time as the order is placed because the customer is being charged upon order placement vs fulfillment. I.e. The credit cards are being both authorized and funds captured in a single transaction.

Magento does not send invoice emails (for any payment method) when a Sale/Auth & Capture mode is being used. If you were to switch to the Authorize mode, it would function pretty much the same as the Check/MO method in that you would have emails sent for invoices and also would have to create them upon fulfillment to actually capture the payment.

The MYSQL error is more a symptom of another issue, than the cause.

In your question you mention that you get a 'long page load' -> this is the real reason for your issues, and then results in the MYSQL has gone away error.

What you need to diagnose is that long delay. What is causing it? It can be a multitude of things.

As an example, on a site I manage, I had exactly the same issues. The end result was that a 3rd party module was syncing orders with an external system using the sales_order_place_after method, which then resulted in a long delay, and the MYSQL error.

You need to debug what that delay is, and solve the root of the issue.

Another example could be when customers sign up for newsletter at checkout (hence why only some are affected) - if you are using an external newsletter signup system, that signup sync could cause delays in the checkout, if not properly implemented.

Your best way to solve this, and identify the lag is to use NewRelic.

ref:

https://github.com/ProxiBlue/OrderSyncQueRunner

http://www.proxiblue.com.au/blog/new-relic/