I was thinking that this was the reason.
I have prepared a little spread sheet of my method if you wouldn't mind looking at it?
A sample of recorded values are in Col A and you will see a frequency a matrix and transitional probability matrix.
As you pointed out row 2 is incorrect.
However the next time the car drives the route a value of 2 could be recorded. And in order to get the average of the two matrices then they would need to be the same size, correct?
Could you suggest a solution to this?