@JackMTaco have a look at this photo. This is a snapshot of the history notes section from a quick flight I just did in the back yard. You can see how the notes progress from the moment the aircraft is booted up till it is turned off. The order of the notes here is what I see every time with a slight exception, In this case, I held the throttle stick all the way to the bottom to shut off the motors - that is the 'Mag #0 Fail' and 'MANUAL CONTROL THE INTERRUPTION'. It will look different if you shut down with the red button. Also note on the left: the first note is where the aircraft first connects with the controller and starts to go through its progress. After the first 'Current Take Off Point Recorded' you see where I manually flick the mode switch to confirm the flight modes concur with what I see on the screen and on the lights off the aircraft to confirm. There are times when I have to a wait a bit longer for this last piece to happen. There is also a second 'Current Take Off Point Recorded' after motor start and before lift off.
Also Note: There are no notes made during the flight and even though this was just a 26 second flight, this is also normal on full duration flights.
As a test, turn on just the controller and open the notes and delete all the history (this does not delete any telemetry files). Then after the controller is on for a minute or so, boot up the aircraft and let it sit for say three minutes then tun off the aircraft while leaving the controller on. Once the aircraft is off pull up your history notes and compare, would like to see what you have.