There was a guiding failure - The guidestar was lost around 01:33
Here's the PHD log for this session where you can see that the guide star was lost
https://www.dropbox.com/s/78yh0391psoexw5/PHD2_DebugLog_2016-06-12_223532.txt?dl=0
Recovery SHOULD definitely have been enabled - There was cloud, the guide star was lost and the target was totally out of frame before the guiding took back over again.
If nothing else, can you tell me from the log whether recovery is enabled?