Harlen’s idea may be right. If your GPS is seeing a lot of SVs then the NMEA 
stream can overrun the second. The time used is that of the end of the the 
first recognized NMEA sentence containing the time field in the cycle.
If you are able to send the commands necessary, you can limit the data stream 
length by selecting just $GPRMC which is often the first sent.
The NMEA command to do that depends on the receiver. What make/model do you 
have?

To check on what your device is sending, cat your NMEA device.

$ sudo cat /dev/gps0      #  that will get the whole stream 

You can check the UTC date from one sentence against another source to see if 
the seconds field is right. It could be that the receiver isn’t counting in 
leap seconds correctly. I had that with one receiver. 

Does your GPS have PPS output? If you have a scope you can check if the data is 
running into the following second. 

Have fun

> Le 23 janv. 2017 à 13:03, Harlan Stenn <st...@ntp.org> a écrit :
> 
> Lloyd Dizon writes:
>> Hi.
>> I've installed a GPS module on a Raspberry Pi and I'm getting 1000ms
>> offsets between the GPS readings and network NTPs.
>> 
>> lloyd@jadzia:~ $ ntpq -p
>>     remote           refid      st t when poll reach   delay   offset
>> jitter
>> =============================================================================
>> =
>> LOCAL(0)        .LOCL.          10 l  447   64  100    0.000    0.000
>> 0.001
> 
> Why are you using the LOCAL refclock?
> 
>> xGPS_NMEA(0)     .GPS.            0 l    -   16  377    0.000    6.229
>> 142.320
> 
> Is your NMEA source identifying the wrong second?
> 
>> *ntp0.as34288.ne 85.158.25.74     2 u   24   64    3    9.810  1004.83
>> 1.687
>> +246.11.25.212.f 162.23.41.10     2 u   19   64    3   10.636  1004.22
>> 1.376
>> +ch-ntp01.10g.ch 81.94.123.17     3 u   21   64    3   10.493  1001.79
>> 3.299
>> -khyber.madduck. 192.33.96.102    2 u   20   64    3    8.703  1001.72
>> 4.474
> 
> Your NMEA source is sending ntpd samples every 16 seconds.  It's filling
> the sample buffer, and the the other sources (are you using iburst on
> these?  You should be...) are taking a while to provide enough samples
> to detect that your NMEA source is "off" by a second.
> 
>> Sometimes it will be the GPS which will have 1000ms offset and the NTP
>> serveurs will have 4-6ms instead.
>> 
>> Anybody has a clue what is going on?
> 
> I think your NMEA signal is identifying the wrong second.
> -- 
> Harlan Stenn <st...@ntp.org>
> http://networktimefoundation.org - be a member!
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"The power of accurate observation is commonly called cynicism by those who 
have not got it. »
George Bernard Shaw

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