You mean little hitches once or twice a minute or so? I think that's just the dreaded microstutter. In general, on PC, when you want a constant framerate you actually have to be able to sustain a framerate which fluctuates between like 105% - 110% of the cap you want. That means that there's enough overhead there that the occasional Windows fart in the background doesn't cause any hitching.
So I'm running Skyward Sword at a constant 30 fps.
Even though the fps counter always says 30 fps, sometimes I perceive a slight hitching or stuttering in the framerate. It's pretty hard to see but it's noticeable, to me at least. I have no idea why it's there and why it's not reflected in the framerate. It doesn't affect the game in any way. Is anyone else incredibly picky and has had the same experience?
If you're only just hitting your 30/60 cap you'll notice a little hitch here and there unfortunately. If you don't mind 25fps you could always go for a 50hz lock which might give you the breathing room you need.