28.03.2017 20:42:17: 450 - Extracting Weather Data from KSFO
28.03.2017 20:42:17: 990 - Wind DIR from weather station : 221
28.03.2017 20:42:17: 990 - Active Runway is set to 19 - Left
28.03.2017 20:43:20: 270 - Extracting Weather Data from KSFO
28.03.2017 20:43:20: 820 - Wind DIR from weather station : 28
28.03.2017 20:43:20: 820 - Active Runway is set to 10 - Left
28.03.2017 20:44:22: 980 - Extracting Weather Data from KSFO
28.03.2017 20:44:23: 520 - Wind DIR from weather station : 238
28.03.2017 20:44:23: 520 - Active Runway is set to 19 - Left
28.03.2017 20:45:25: 640 - Extracting Weather Data from KSFO
28.03.2017 20:45:26: 180 - Wind DIR from weather station : 294
28.03.2017 20:45:26: 190 - Active Runway is set to 28 - Left
28.03.2017 20:46:28: 380 - Extracting Weather Data from KSFO
28.03.2017 20:46:28: 930 - Wind DIR from weather station : 158
28.03.2017 20:46:28: 930 - Active Runway is set to 19 - Left
28.03.2017 20:47:31: 090 - Extracting Weather Data from KSFO
28.03.2017 20:47:31: 630 - Wind DIR from weather station : 101
28.03.2017 20:47:31: 630 - Active Runway is set to 10 - Left
You were initially cleared for 19L (at pilot's discretion), but the log shows rapid and frequent wind shifts (every minute or so) at your destination airport, causing PF3 to repeatedly change the active runway. I don't know if the constant wind changes had anything to do with your not being notified, but the rapid wind shifts are an issue experienced by other users and can be addressed by adjusting settings in your weather add-on. If you have already made the changes to the settings in AS2016, I'm unsure of the reason for the constant wind shifts.
As far as the active runway being changed after clearance at-pilot's-discretion is given, I'll have to defer to Dave on that, to see if something needs to be changed.