I had this problem. I emailed Woothemes support, who suggested re-saving the Permalinks. So this would be a simple thing to try first.
For me that didn’t work. What I did in the end was get the PDT Identity Token from PayPal and putting that in WooCommerce settings. So it was using PDT rather than IPN for the notification of the payment. And it worked.
Let me know if you need an explanation of how to do any of this.
Christine F. Abela
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