then I had to restart the computer.
You don't have to restart it immediately...
MyDefrag is able to resume its work using the same script with any of default scripts but generally it's able to do so "cleanly" only if the disk contents did not change since the script was interrupted,which is never the case on a system disk. If there is change, zones may get placed at slightly different positions or file order may change and this may induce additional operations performed by the script.