Magento – new orders are not showing in orders grid

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/

after creating programatically invoice you have to set state and status for that

$invoice->getOrder()->setIsInProcess(true);
$order->setData('state', Mage_Sales_Model_Order::STATE_PROCESSING);
$order->setStatus(Mage_Sales_Model_Order::STATE_PROCESSING);
$history = $invoice->getOrder()->addStatusHistoryComment(
    'created invoice', true
);
$invoice->sendEmail(false, '');              
$order->save();

second solution

you use the default magento state with custom status that will solved you problem.