I think 12k RPM is too slow. Try something like 18k. Is it a 1, 2, 3 or 4 flute cutter? I normally use 4 flute cutters on aluminium with the RPM and get very good results. I don't think your problem is spindle run out but can be caused by vibrations. I don't know how your machine looks like, how rigid and well made it is and so on, but to me looks like you have a vibration issue. Are you using any lubricants?