It sounds like the fork/wheel is flexing enough just enough to induce a bit of rubbing. Take a look at the disc through the caliper and see if the disc is true. if not you can tweak it a bit to straighten it. Also check if the inner pad is properly set up.
With these mechanical disc systems there is a specific way to set them up. Most people do not turn in the inner static pad enough and after a while the static pad wears a bit and the rotor begins to wear against the caliper.
Loosen the brake cable fixing screw and the screws that fix it to the frame.
Turn in the inner static pad to the point that the inner pad is sticking out about half its width. A little more is ok since you'll back it out later. This step is important in properly centering the caliper over the disc.
Pull the cable tight and fasten the brake cable fixing screw.
Grab the brake lever and tighten the caliper fixing screws.
Let go of the lever and look at the caliper from the back. If it worked right the inner pad should be right up against the disc and the outer pad should be recessed in the caliper.
Back out the inner pad a little so it does not rub the disc and then make your cable adjustments.
The closer the inner pad is to the disc the more solid it will feel and the less the disc will have to deflect.
In the end it should look something like this.
not this
