12 extra layers should absolutely not cause a 40% increase in CPU use, especially on an i5. My game has somewhere around 20 layers and when running on an old amd Athlon 4400+, the CPU low point is around 35%, and that's also running the thousands of events in the event sheet at the same time (not all the events are running each tick, of course).
I'm not sure what's causing it, though. Are you using layer effects? Forcing the layers to have their own texture? Try making a copy of your capx and experiment, delete everything except the layers, try deactivating all the events, turning all the layer's settings back to their defaults, etc.