Scenery and Terrain slider have the biggest impact.
As I said, your CPU may well work fine normally, but used heavily O/C CPUs get much hotter, and CFS3 uses the CPU and memory very much so it will probably show more than in other situations/programs. Same with the memory too if that is pushed it can overheat. So you can try to lower the CPU o/c perhaps and try? Also if you have CPU throttling and other intel settings in the BIOS enabled it may be doing just that during those pauses.
Try installing HWMonitor and check temps under load on parts (doesn't show memory though).
Also if it's a long pause, but works fine after perhaps other programs in the background are running every so often? AV scans etc?