I found this link Mysite signin repeats in IE that sounds like the problem I am having right now, but none of the answers is the right solution for me.
I have created MySites on Port 80 (I got two webapps at 80, mysites and my portal) and created a root site collection with the MySites Template. I have run the UPSA and synched all the users from the AD.
When i enter mysistes directly trough its link, or via my portal webapp, I have to sign in, which is okay. But I cannot sign in with any of my user accounts, they just does not get recognized.
I found this http://blog.solutions2share.net/2013/01/cant-login-to-sharepoint-2013-site-when.html guide. After i do the last steps and iisreset, I am able to log-in. But why is this necessary, and I am doing this on a virtual machine, will this be applied to all clients ?