It's a glitch in the optimisation system that they tried to bring in before, but they later removed due to a big glitch with it. The re-intorduction of the system caused the stuttering (Everyone wants to call it a framerate issue). Basically it tried to reduce the amount of stuff rendered at once, you can see this in action by warping around the sanctuary and watching it have to load before you arrive in the next place. Before the re-introduction of the system it didn't have to do the level load.
Although I do not recommend changing the file, I have to say it did work for me and I will not be changing it back until SOE relise that this system is causing it and do something to resolve it.
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