Corrections to my test below.
1. Add the attributes controlling quantity first.
2. Go into Products with Attributes Stock and setup stock. IMPORTANT Do this even on attribute values that have no stock presently, set to 0, but you may add later.
3. Now go back and add the additional attribute names/values to the product.
Example:
Is having some attributes that are "read only" to give additional information about a product. But they don't effect overall quantity. If you attach two attribute names to a product when you go to build the quantity with attributes by stock it will build a cross table of multiple values and the code above won't work.
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