Turned out that (for who knows how long) I wasn't feeding in the minimum correlation angle / distance into the code that makes the mesh for the correlation code. For some reason when I called the function I had hard coded 0.0 as the minimum correlation angle/distance instead of corrmin. So this meant that all objects with correlations less than corrmin were all put into the smallest bin. I don't think this exactly explains the observed spiky behavior, but now that I've fixed that I am going to see if things work better.
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