I've looked at the core-email queue in the SQL database and only "new order" and "update order" are being sent in the queue for the CRON job.
I've read somewhere that there might be an exception and that only transaction-email are being sent to the queue and the rest is being handle by the server. Magento 1.9.1 - Emails being sent by the new email queue?
So, I found this guide to see how to debug it http://www.hummingbirduk.com/magento-not-sending-emails/ and followed the steps and was able to see receive test emails from the server. So the problem lies in the magento configuration and settings.
I've been spending quite some time figuring the problem and now I am out of idea and was wondering if someone my have hints about how to solve this problem or what step could I take to narrow the solution.