Answer: The reason why Boyle's is not obeyed is because the size of the gaseous molecules is more appreciable compared to the volume of the container containing the gas.
Explanation: At such high pressure of 1000atm , there will be high amount of gaseous molecules in terms of numbers and the volume of the gas will not be able to be decreased as if the gaseous molecules were dimensionless. The piston of the container containing the gas will not be able to pushed down much because the molecules will require an appreciable space.