If you find yourself in a situation where you have received a PayPal notification email after an order has been placed on your store - but the order is not appearing in your dashboard, the issue may be down to your Postage Calculations setup in your PayPal account. Another symptom of this issue will be that you'll find the Shipping has either not been charged by PayPal, or a different amount has been charged.
The solution to this issue, is to either clear your Postage Calculations settings, or specifically allow for PayPal transactions to override the values you have set. Here we detail the solution that will achieve both of these steps and resolve the matter:
1) Login to your account and click on Seller Preferences which will either be on the left hand side of your PayPal dashboard, or within your account settings menu. Note that the exact location of these steps may vary based on the account type you have.
2) Click to edit 'Postage calculations' - by clicking the 'Update' button on the right hand side
3) Click 'Clear Settings' at the bottom of the form to reset your Postage Calculations.
4) Enable the following option: "Click here to allow transaction-based postage values to override the profile postage settings listed above (if profile settings are enabled)." by making sure the checkbox is ticked. Then, click Save.
If you have been affected by this issue - we advise that you speak to PayPal, quoting the corresponding transaction ID of the order. Note that once this is corrected, it will only apply to orders received from that point forward.