It was some extension I was using, it cleaned cookies as well. I am now using another extension where I can whitelist domains for cookies to be not deleted and it works like a charm. Thanks for the help any way!

This problem is now solved.

Not yet, I'll try it tonight with a new profile and see if that works. I'll update this when I know more.

 Am I the only one with this issue? If that is the case it probably has to do with my current firefox installation or configuration.

That's why I disabled both the native cleaner and click&clean to see of that caused the issue, that didn't help me unfortunately.

Yes, I cleaned them. I've restarted my browser several times. Even disabled all the browser cleaner options as well and click&clean extension.