-
Sorry, what led to the conclusion the brakes are hydraulic? This can be usual mechanical disc brakes thing on a road bike with less lever movement, not enough space between pads and not a very straight rotor. Had this all the time when using BB7 roads. Shimano CX77 fixed the situation immediately
Hydraulic disc brakes do how web tend to fix themselves due the nature?..
Just straighten the rotor maybe :)
The two most obvious things are excessive disc runout and insufficient pad retraction.
Park Tool have a decent article on measuring and correcting runout. It's less likely with floating rotors.
Insufficient pad retraction is usually a feature of hydraulic brakes which have been rode hard and put up wet, causing the pistons to stick in the cylinders due to contamination or corrosion. If it's not terminal it can be fixed, sometimes just by external cleaning around the piston seals, otherwise by rebuilding with new seals and possibly pistons. If the cylinder bores are damaged, it's terminal and you need new calipers.