Hey guys,
we are running on meteor 3.1.2 for a week now and did not have any problems on this second attempt. The most relevant changes were, a new meteor version, converting all Meteor.call to Meteor.callAsync and removing quit a few unnecessary subscriptions. We did not really fancy investigating this any further on our production environment, so we are not sure what exactly fixed the issue in the end. Just wanted to provide the promised updated in case anyone else runs into similar issues.