Not sure what you are doing or if perhaps you dont understand that you have a choice of plotting either 6 digit or 4 digit grid squares.
If you choose to display 4 digit squares there is no point in plotting 6 digit ones because you chose to show just the major squares and of course that includes ALL of the six digit squares within the major 4 digit square as below:
If however you select 6 digit squares in the program config it will only display those squares because you have not worked all of the squares that complete a 4 digit square, as below:
Its your choice but its self defeating to try to display both and confusing to the eye
The program is functioning as designed and these screen shots are taken using the latest release