...I'm beginning to think the scratchplate is just bowing slightly. it now sits flush at the top and bottom, even around the knobs and switch where the bulk of the wires are, but refuses to sit flush around the middle...
If you're certain that everything's clearing the routing, and you're able to push is flat in the middle with light pressure (like with one finger) I wouldn't worry about it. It will be fine once you screw it down at final assembly.