In the past week some customers have been reporting that PayPal processed bookings have not been auto-confirming. From those reports it would seem that this issue has been occurring no earlier than the 1st July 2015.
The issue is related to a PayPal url used for verifying the authenticity of PayPal Instant Payment Notifications (IPNs), which until the 1st July 2015 had been operational. If a received IPN cannot be authenticated, the booking remains at pending. Event Organiser 1.10.4 fixes the issue.
It is recommended that you review any pending payments from the 1st July 2015 to the date you update to 1.10.4 to check for any (erroneously) pending bookings.
This issue affects the PayPal gateway only.
I apologise for any inconvenience caused.