I've had my Opencart site working fine for well over a year, after Christmas 2012 I came back into the office to find the standard Paypal messages (about payment settings being incorrect etc.) and all my orders going into the Missing Orders and not showing up in the Dashboard.
Now I know for a fact I never changed anything in Paypal, but I've double checked everything today as one of my other shops (wordpress and not many orders) that also uses the same Paypal account had a failed return IPN so I didn't get the order in the shops backend.
Lo and Behold my IPN setting had gone from enabled to disabled! - without me going near it. I've changed it back and can confirm I now see orders in my Dashboard in 1.5.4.1
Happy

Hope this helps others who are having the same problem