I'm having that problem too, I'm using Windows 8 64 bits with the last version of Java, it happens to me with all the versions of minecraft and not only with the new launcher, I tried some other launchers like "Multi MC" and it still happens.
I'm thinking that is a process in our pc's that is forcing somehow minecraft to minimize, but I can't figure out what's exactly doing that.
I forced a crash with F3+C right after minecraft automatically minimize.
Don't know if it is useful. (I attached the crash)