Unless you are in an area with good reception, it is quite difficult to deal with WWVB reception errors. In April 2010, Ed Nisley published a good Arduino WWVB receiver article in Circuit Cellar, issue 237, called "The Totally Featureless Clock". It is reported to handle the problem fairly well, but doesn't work well in my area.
You can download the code here.
The code uses a primitive edge-triggered interrupt method to time pulses, and then examines the result for illegal pulse widths. That is very sensitive to noise, and could be vastly improved by continuous sampling, but I haven't got around to it.