Sale Notifications being enabled/disabled would not be sporadic, affecting some sales and not others; it would affect notifications for all your sales across the board, but we fixed that bug over a month ago and have not seen it return, so something else is probably happening for you.
First, check your Spam folder and mark the notification messages as Not Spam if you find them there. Also bear in mind some email providers often have significant delays in sorting inbound email delivery to recipients' actual inboxes, so they may yet show up in time.
Next, check your E-junkie Transaction Log to see whether the un-notified sales are listed in there. If not, that indicates we didn't even process the order yet, so we would not have sent any notification, as that gets generated when we process the order. Presuming you're seeing payments in PayPal that aren't showing up in your E-junkie Transaction Log, this troubleshooting page will help you sort out the reason for that: