The root cause is one of the following:
1) PayPal is taking long to send the IPN (Instant Payment Notification) to your server (this is most likely the case).
2) Your server is taking long to send the emails.
This usually doesn’t happen all the time but sometimes PayPal can take long to send the IPN. The WP eStore plugin won’t send out the download links unless it receives the payment confirmation from PayPal. Settings up the links on the “Thank You” page is a good alternative for this.
I have sent you the fix for the apostrophe problem.