Quote Originally Posted by securit View Post
Its running PalPal Express checkout rev1.5.4
You said you're using Express Checkout, but the only logs you're posting are from IPNs.
Transactions originating as Express Checkout transactions do not get added to your store via the IPN process. In Express Checkout mode, he IPN process is simply a notification tool to update the status of transactions.

So, if your store doesn't have the transactions stored properly, then the rest of the checkout code that happens immediately after PayPal receives the "complete this transaction" instruction, is failing. Presumably because that part of the code on your server is altered in some way.

While comparing all the paypal files against originals is useful, it doesn't tell us anything about the ways in which your store has been altered from original code and original function. And yet therein likely lies the answer to your unique problems.