I don't know if this triggered the problem, but I noticed that you pressed hotkey #0 twice during departure:
12/27/2016 10:15:39 AM: 210 - ****** HotKey #0 detected!
12/27/2016 10:15:40 AM: 380 - Transcript: 'Departure November 819 Out of 2 thousand for 3 thousand IFR '
12/27/2016 10:15:47 AM: 570 - ****** HotKey #0 detected!
12/27/2016 10:15:49 AM: 770 - Transcript: ' November 819 Squawk 2631 ' |
But it could be a problem in PF3 as well, there have been some fixes regarding initial altitude problems in the current beta.
In such situations it should be possible to request a different altitude.