I've just posted a summary of the issue and where things stand, along with some helpful/informative related links, in this other forum thread:
As of 1:25am PST this morning, PayPal has caught up with sending their backlog of IPNs which were delayed due to the problems at their end yesterday morning, so we will not be receiving any more delayed IPNs from them, and we are now receiving IPNs for new payments almost immediately after checkout (as usual) and processing those orders accordingly.
If you are still seeing some completed payments in your PayPal account history which are not appearing in your E-junkie Transaction Log (indicating we have not received IPN for those orders and thus have not processed them), first see if this post may be relevant to your situation:
See if you can resend affected IPNs from your PayPal IPN History (after temporarily reversing any price changes you may have made yesterday, as described at the link above) -- see the third main bullet point here for instructions on how to resend IPNs:
If you cannot resend the affected IPNs from your IPN History, see if you can at least get a copy of the full IPN Message from there (click on the Message ID) for affected transactions and send that to our support team for further investigation:
If your main concern is just delivering any overdue download or code purchases, and you're not concerned about doing the troubleshooting described above to have our system process those orders automatically, you can use "Send free download link / code" in your Seller Admin to fulfill those orders manually.