The present invention is directed to a method and apparatus for improving spiral-based position correction system stability via kernel frequency component modification. In one embodiment, a disk drive includes a disk surface with servo information written thereon, wherein the servo information includes repeatable runout. The disk drive includes a servo system having an error transfer function. Frequencies, where the error transfer function may experience phase changes, are determined and the direction of such phase changes are also determined. A kernel, which is used to calculate position correction values to compensate for repeatable runout, is provided. Phases of frequency components in the kernel, which correspond to the frequencies where the error transfer function may experience phase changes, are rotated.