As I said. Don't use Insert Into Array. Use Build Array to put the data at the end.
Put the new updated array onto the wire going to the shift register. Your file gets updated, but the copy of that you maintain in memory doesn't get updated.
I think you are losing your first row of your data because you are failing to put the header row into the file. So when the file gets read at the beginning of the program, when the first row gets stripped out to eliminate the header, you are losing the first row of real data because the row it is trying to strip out isn't there. Is there really a reason that you need the header row in the file? I'm going to recommend a change where you don't put that in the file at all.
Also, you haven't said what is the purpose of the index column?
Here I cleaned up the file. I changed the timeout method I was doing to get the file read at the very beginning, to just reading the file before the while loop starts. I left the header in the array that is held in the shift register, and just used array subset to get the array without the header showing for the sake of the front panel. I did the new index calculation and replaced your Insert Into Array with the Build Array function.
