When orders placed with the "PayPal Website Payments Standard/IPN" module don't show up in your store, that's a direct result of a problem occurring when PayPal's server cannot talk to your server to tell it about the new order.
Recommended course of action: Click "Remove" on "Website Payments Standard", and click "Install" on "PayPal Express Checkout".
Express Checkout is much more reliable, as it doesn't depend on PayPal's archaic IPN architecture to get orders into your store.
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