Before going any further you need to check if the machine is moving the distance it's been told to move. If the steps per setting are wrong you'll never cut correctly.

So Zero the Z-axis up in the air and make a mark or measure the distance from the tool to the table, then in the MDI type G1 Z-10 F1000 and measure if it moves down 10mm.

If it moves 10mm as instructed then the most likely cause is the touch plate height in your script is wrong.

The only other possible cause is you have a tool height offset set in the tool table but this would require your code to uses a G43 H# value so it calls a tool height offset. Easily checked by looking at the tool table.