Got problems too. Firmware has not fix error => 3/4 cores working, 1/4 dead.
Have you called KNC? I know O'rama says that no customer support emails get ignored, but I've found it the case that they don't all get replied to - at least not in a timely manner.
I don't want an RMA at this time --> Mining Time loose. (Saturn)
I hear you...if it's running at 75% speed then taking out a card and running at 50% speed isn't great. Just for kicks, have you tried it with 1 card disconnected to see what speeds you get? I got better speeds with a bad card removed than with 1 card running on my first Jupiter.
And bitcoinorama - if you are reading this, here is the reason that KNC needs to improve the RMA policy. It hurts us to send semi-defective equipment back until much much later when the equipment is mining fewer BTC per day. It's better for KNC to wait until orders have slowed down dramatically, I'm sure, but it's not better for the customer.