Make sure that the 1 PPS  output is enabled...  It can be turned off by 
software and that mode can be set in EEPROM.

Also,  many scopes have great difficulty showing a 10 uS pulse at a 1 PPS rep 
rate.  Digital scopes might not sample it in normal display modes (envelope or 
glitch capture mode can help).  It can easily get lost on an analog display...  
                                     
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