So they replied that they checked the servers and everything should be working now. However it is not, it is still redirecting to wrong pages when using other than ugly permalinks. I guess I am going to wait if any future WP update will fix this.
Thank you for your reply. I asked my host and currently I am waiting for an answer. I am pretty curious what they are going to reply 😀
My hosting is on Axfone.eu and they are running ISPConfig if you are asking that