That preference is only applicable to certain parts of Krakatoa involved in the rendering process. It has no effect on saving particles, especially when running particles through external systems (ie. Particle Flow, Thinking Particles, Modifiers, etc.).
Some people have had success using Deadline to start multiple instances of 3ds Max on the same machine in order to use more cores. Depending on the I/O requirements of your scene and the fact that starting Max is often slower than partitioning a frame in Krakatoa, your mileage may vary.