Is it possible that you set the clock initially using the PyClock application in your local timezone?
ntpdate runs in UTC always, and the timezone used by the Zero is Central European Time, so when you set your time, it was recorded as being the time in a timezone 5 or 6 hours to the east.
For reference, I just checked the time on my Zero, which I set in August, and it was "20:43" when my local time was "19:53", but my Zero is really 10 minutes 36 seconds late, not 49 minutes 24 seconds early, because I set it when Daylight Saving Time was in effect, and now it's not. And when I ran ntpdate, I got an outrageous offset like you.
My timezone is GMT-5, or -4 in the Northern Hemisphere summer.