Hi Nicolas,
It looks like the problems is spotted now and it has nothing to do with the plugin, the Hikashop update or Joomla!, but, as you mentioned, a network problem.
I've been in touch with our hosting company now and they have located a 'hop' server in the routing system that is loosing packets in the routing process. Since the datacenter, where the servers are located, is having trouble in fixing this issue with a couple of servers that use this hop server, we are migrating our system to a new server that isn't affected by this problem.
As soon as it happen, I will revert to the latest plugin that is part of the stable package and try to resend the IPNs. If it works, as I suppose it will, then I'll let you know.
Thank you