no. normally windows don't set any limits. But Windows won't priorise your encoding the highest possible way.
So you encoding-process will be stopped, if there is a process that needs to be done and has a higher priority.
On top of this, encoding-speed can vary depending on the content of the video.
if you got large Parts within one color, x264 can encode faster than on pictures with many different shapes, colors etc.
just like jpeg.
IO shouldn't be a problem, since you probably won't use more than 10MB/s and if your HDD don't get that fast, look for another server.
12FPS isn't that high - especially for a 6core CPU.
what encoding-program do you use?
have you checked, that you use all 6 Cores?
define "slowest preset" ?
