Works fine for me 10.0.2 on MacOS 10.8.5.

You might try a "clean start" of Mathematica in case an initialization file has bad parameters.
http://support.wolfram.com/kb/12464

Using Mathematica 10.0.2 on Windows 7 the code appears to work resulting in the following output:

allPts before being passed to centroid[]: {{0.00809987,0.80996,0.482635},{0.582,0.18269,0.497061},{0.00318512,0.00947919,0.00954099},{0.33409,0.237663,0.00409993},{0.125128,0.168651,0.0668875}}

ptList in centroyd: {{0.00809987,0.80996,0.482635},{0.582,0.18269,0.497061},{0.00318512,0.00947919,0.00954099},{0.33409,0.237663,0.00409993},{0.125128,0.168651,0.0668875}}

centroyd: {0.210501,0.281688,0.212045}

ptList in centroid: {{0.00809987,0.80996,0.482635},{0.582,0.18269,0.497061},{0.00318512,0.00947919,0.00954099},{0.33409,0.237663,0.00409993},{0.125128,0.168651,0.0668875}}

centroid: {0.210501,0.281688,0.212045}