I can see them saying they won't withhold any more until your new 20% election is used up - for example, salary during the error period was 50,000 - they should have withheld 3,000, but instead they withheld 6,000. So there is a 3,000 excess. Now your new election is 20%. Until such time as 20% of your pay under the new election equals 3,000, they don't withhold anything. That seems like a reasonable and appropriate correction.
It does not seem reasonable to refuse to honor your new 20% election until the "correction" is made based upon an ONGOING 6% assumption, even though you have elected a new percentage. As alluded to above, I would push this, and ask for a WRITTEN explanation.