So I haven't quite nailed this down.
This only began occurring for me after yesterday's patch, build 6723. As far as I can tell the exact same thing is happening to me, but only in instanced zones and never in the open world.
What happens: I will stick right around 30 fps without any serious fluctuation but the screen will stutter for just a fraction of a second at completely regular intervals without deviation, as described by the OP, but perhaps not in second-long intervals specifically.
I was questing in the open world without any issues when I queued up for Walatiki Temple. Once I got in I experienced nothing but this regular stutter, and it was immediately apparent that it wasn't lag and I could also see that my framerate hadn't dropped. Upon finishing I was dumped back into the open world and had no stutter whatsoever. I restarted my PC and tried another round of Walatiki Temple, which gave me the exact same issue with the exact same timing. I stayed in the open world to quest for the next several hours until I got to The Steady Traveler instance in Deradune where I had the same experience again, only this time without any other players in a relatively small room seemingly without any relevant drains on my system.
I, too, thought that it could be addons so I reset the addons to Default which removed all the player mades. Instead of going away, the stutter interval changed; it was just longer between each stutter by about 1.5-2x what it was before. Reloading all the player made addons seemed to bring it back to the original stutter timing.
Finally I found this post and tried Alt+Z. I was surprised again to find that the stutter almost seems to go away, or rather it turns into something that I would be more inclined to say looks like lag. If there's a pattern to the stutter when the UI is off I can't notice it, but I am still noticing the same tiny frozen frame for a split second here and there in a way that I just don't experience in the open/non-instanced world.
Windows 7 SP1 x64
Intel i7 3.20 quad
12 GB DDR
2x ATI Radeon HD 4870, xfire