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I believe the pointcloud is properly aligned, but not the container holding the point clouds.

Let's assume you have a point cloud of type PointCloud. Initializaing a std::vector like this will cause alignemnet errors:

std::vector<PointCloud> my_deque;

The proper way to initialize is:

std::vector<PointCloud, Eigen::aligned_allocator<PointCloud> > my_deque;

I assume the same holds for other types of stl containers, such as a deque. More information here