Ok I've got this issue at the moment, A client pays with PayPal, however the transaction isn't recorded in the database, and the payment hasn't been added to the invoice. 
  
Cron jobs have all ran.  
  
 Cron Job Error Log: 
  
Apply Payments to Open Invoices	Start Date: Sep 10, 2013 5:25:05 PM End Date: Sep 10, 2013 5:25:08 PM
Output
Attempting to apply credits to open invoices. Unable to apply pending credits to transaction . The apply credits task has completed.
I had to record the payment manually: The payment was successfully recorded for £0.98.