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Hi, I have been placed in an endless loop of no help trying to get help with this problem from PayPal. Does anybody know why payments made with "PayPal" are not posting but payments made via credit card check etc do post to my server? IPN notifications are only failing if paid via a PayPal account to our shopping cart.
IPN can be tricky to troubleshoot. I would recommend checking out this guide I wrote on how to test IPN. If you follow those steps you should be able to figure out what's going on.
Mainly, the first step in your case would be to check the IPN History to see if IPNs are indeed being sent for those transactions, which I'm assuming they must be, and see what the result of the IPN was. You may find the result is a 500 which means you've got some sort of failure happening in your script, in which case you can follow the steps in my guide to help troubleshoot that.
If you see the IPNs are being sent with a 200 result then that means the script must be completing successfully, but if you're not seeing the actions occur that you expect based on these IPNs then you would need to double check your logic. Again, the guide provides details on how to troubleshoot this sort of thing.
Hope that helps!