It's probably a good idea to take a series of test images and post a representative image here. Post a full image and a 100% crop so we can see the problem. There are a lot of sources of softness.
Having a problem with multiple lenses would indicate a camera problem, a technique problem, or a setting problem. But if half of your images are sharp and the other half are soft, technique seems to be more of the issue. A camera problem would show up in every image - not half your images. Fine tuning is lens specific and should not automatically be required for every lens.
I would not rule out settings. The increased resolution of the D600 viewed at 100% show softness that might otherwise have not been noticed - especially shooting wide open. For example, the 70-200 shows softness at f/2.8 - and does not reach optimal sharpness until the f/4-5.6 range. Also the FX sensor effectively provides DOF about 1 1/2 stops wider/shallower than the same settings for DX, so it's easy to not have enough DOF for an image using settings that were fine on DX cameras. The 85 f/1.4 is known for both a shallow DOF and nice softness to the subject and background - but it may not be the sharpest lens.
I've had a D600 since initial release and have not seen a focus problem.