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Hmm -- to summarize, it sounds like we've established that PayPal requests are coming in to OJS, but OJS is not flagging payments as completed. There are basically two situations in which this would occur: OJS is encountering a fatal error (which should be in the error logs), or OJS is encountering an inconsistency in the payments, which should result in an email. I can't think off the top of my head of a situation in which neither of those is happening, but in any case, the next thing I would do if I were debugging this is to start modifying the PayPal plugin to log more data when a request comes in, by using PHP's error_log function. That would help to narrow down what's happening to the IPN requests.
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