I have exactly the same problem...
Hello, Wishy:
I have exactly the same problem you did right now. When customer place an order onto my side and pay with Pay IPN, I can receive the money into my paypal account, but I don't receive any email from the Admin, and there is no new order showing in the "Order" in Admin.
Right now I am following Ajeh's suggestions and reintall a brand new Zencart 3.17 onto my server and use the original Zencart database, without adding any modules. If this problem still exists, then it must be something wrong with Paypal IPN. I will let you the result after I finish the intall and test.
Lina