Unless something's changed since 2.49, when you do an equality check for vectors, it does an element-wise comparison. When you use the inequality operators, it does a magnitude comparison.
http://www.blender.org/api/249PythonDoc/Mathutils.Vector-class.html "Comparison operators can be done on Vector classes: >, >=, <, <= test the vector magnitude ==, != test vector values e.g. 1,2,3 != 1,2,4 even if they are the same length"
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