...or maybe I'm not seeing things .  Try this code in there instead:

            if vx > limits[0] and vx <= limits[1]: row = r[1][0] #row is inclusive to right
            if vy >= limits[2] and vy < limits[3]: col = r[1][1]#col is inclusive toward bottom
            if vz > limits[4] and vz <= limits[5]: depth = r[1][2] #depth is inclusive toward front

...it's possible that the comments are no longer true (I didn't double check that), but this seems to at least get the missed matches in the right sectors.

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