Primary cards are always going to perform worse as they are stressed by the OS, your browser, background apps and so on. Also,the -H flag could cause it so try -H 2 to exclude the CPU. If you're not using risers, chances are one of your card is hotter than the other, or at least requires a higher fan speed to keep it at lower temps so the fans are using more power on one card which very well means lower core frequencies when it comes to kepler. And those are not the only possible explanations, but my brake is over...