Why is my application freezing every couple seconds?

So I am currently building an application for a CAVE, four walls and a floor all in stereo 3D. I have put together a simple test scene with a plane and some animated characters walking around. I baked a navmesh into the plane, and set up the characters to wander around on it. The animator I am using only has one state, walking. The wandering script just picks a new random point whenever the character reaches their destination. I need to run in OpenGL mode for our stereo to work properly, since we are running on Windows 7 and don't have access to DirectX stereo (correct me if I'm wrong on that). The problem I am running into is that with a few characters in the scene, ~10, the app starts to stutter. It will appear like everything freezes, but then everything will jump forward to where it should be. It seems like the frames are happening, but just not being rendered. I can't run the editor in OpenGL mode to see if there is an issue there, and without running in OpenGL mode, I have no issues and can have hundreds of the same characters running around and get good (~50-60)FPS.

So my questions are, what would cause the framerate to stutter like that? Is there any good way to narrow down what would be causing this in a standalone build? I have tried testing with various characters/animators/navigation scripts but the only things that seem to affect it are whether the app is in OpenGL and if there are more than ~10 characters. What part of OpenGL would cause this problem?

I would really appreciate any help at all, since this problem has been troubling me for awhile now.