You may be over softening the corners, they only need enough slack to take up from the initial rolling.
As far as making them perfectly flat, put the big wrench on the short or long bar corner that is high, and pull in slightly, then re-check for flatness.
How you tighten the bolts will have some effect on flatness, so when you are done tensioning the frame, snug all the bolts first, then go back around and torque them.