Have you noticed a difference between the time displayed on your Global Positioning System (GPS) receiver and the time from the U.S. Naval Observatory's Master Clock? There are several things that could cause the difference you see.
GPS broadcasts its own GPS system time and a correction to Coordinated Universal Time (UTC) as kept at the U.S. Naval Observatory (UTC(USNO)). GPS system time is a uniform time based on International Atomic Time (TAI). UTC(USNO) is a non-uniform time that is periodically adjusted by adding or subtracting leap seconds to compensate for the changes in the rotational rate of the Earth. (Detailed information is available on the World Wide Web at http://tycho.usno.navy.mil.)
On January 6, 1980, the two times were identical. Since then 13 seconds have been added to UTC(USNO) and GPS system time is now ahead of UTC(USNO) by that amount. Most commercial and some military GPS receivers automatically apply the UTC(USNO) correction so that what you see displayed is UTC(USNO) even if it says GPS time on the display. But there are some receivers that allow the user to select if they want GPS system time or UTC(USNO). This may be one possible cause of a time difference between GPS time and the USNO Master Clock. If you have one of these receivers, you must check its mode of operation to make sure you know which time is being displayed.
Another potential cause of a discrepancy could be the refresh rate of the GPS display screen. Most GPS displays have a lag time of one half to two seconds. Others do not show each second but skip one or two seconds. This depends on the quality of the processor in the receiver.
The bottom line is that you should be sure you know what time your GPS is displaying and how accurate the display is compared to UTC. If you are using your GPS time display as a basis for your JN or N sights, you should first compare the displayed time to a known accurate source such the USNO Master Clock or WWV. If there is a difference, the difference should be recorded as watch error, the same as you would do for any other time source.