Thanks everyone for reporting this; I've referred it to Development for investigation.
PayPal hasn't posted notification of any known issues with IPN at their end, but you can check whether IPNs have been sent and, if not, resend them -- see the instructions under step C, item 2 here:
If the IPN shows a status of Failed, tick the box next to each failed IPN and click Resend, which should then have us process the order manually.
If the IPN shows a status of Sent, but you're still not seeing the order in your E-junkie Transaction Log, you can use Send Free Download Link in your Seller Admin to generate a link manually, then copy and past the link generated there (as @AlexanderG suggested above, thx!). Please email our support team with the Transaction IDs of any such orders (where IPN shows as Sent but order not logged in E-junkie), so we can refer those to Development for investigation.