Labelled equations are not rendered when re typeset
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There is an issue with updating and retypsetting numbered equations:
Labelled equations aren't rendered at all.
The counter on unlabelled but numbered equations that are updated keeps increasing on every pass, throwing off the numbering sequence of all equations.
See here: http://jsfiddle.net/ZCEQ7/
This is the correct behavior. If you re-typeset a container that has an equation with a label, MathJax will see this as being a second equation with the same label and will throw an error (but the noErrors extension will trap that and simply display the original TeX code). Similarly, the other equations with numbers will be seen as new equations with new numbers. Because you could be typesetting two containers in succession to get the complete page, MathJax does not reset label and equation numbers between typesetting those containers.
If you want to reset the the labels and numbers, use
MathJax.Hub.Queue( ["resetEquationNumbers",MathJax.InputJax.TeX], ["Typeset",MathJax.Hub] );