That's JTAlert's "guess" of when the QSO start from the "new QSO partner" which 
can be horribly wrong as you've found out.
WSJT-X r7430 added it's own TIME_ON field and JTAlert 2.9.0 now uses that 
instead of it's own guess.
de Mike W9MDB

      From: ANDY DURBIN <[email protected]>
 To: "[email protected]" <[email protected]> 
 Sent: Tuesday, February 7, 2017 10:04 AM
 Subject: Re: [wsjt-devel] WSJT-X: QSO start and end times
   
 <!--#yiv6121361698 P {margin-top:0;margin-bottom:0;}-->"I do believe it's 
JTAlert 2.9.0 that has the TIME_ON fix and you have to be using r7430 or 
greater.
de Mike W9MDB"

I browsed the JTAlert change log:
JTAlert Ver 2.5.0 13 Nov 2014
- QSO Start time field in Log Fields area. Populated with the utc time when     
  a new QSO partner Callsign is detected. If it contains a value it will       
override the time provided by WSJT-X and JT65-HF logging event.

I could find no record that indicated this behaviour has been changed.

73,Andy k3wyuc



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