Hm so if I'm understanding correctly: For a very short time after starting up the computer, the problem doesn't occur, then the problem starts happening, but then stops after another 5 - 10 minutes?
The loading icon in the video and the labels appearing is definitely the biggest clue.
I wonder if the debugging instructions in this thread might help: Changes to folders are not being detected
Perhaps that will show some revealing information about what it's actually doing when the loading is occurring.