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It was recommended by @nghia that I try and make the percepts a constant size. Sure enough, if I fix the dimensions and type of the cv::Mat members of percepUnit, then the leak disappears.

So it seems to me this is a bug in OpenCV that effects calling clone() and copyTo() on Mats of different sizes that are class members. So far unable to reproduce in a simple program. The leak does seem small enough that it may be the headers leaking, rather than the underlying image data.