I suppose it depends on what you mean by "skipTags, ignoreClass, processClass do not work".
When you specify an array of elements for MathJax to use, then each element will be processed in turn. That is, the contents of the element will be scanned for math, and within that element, skipTags, ignoreClass and processClass are respected within that element. But the no classes or tags OUTSIDE the elements you provides are taken into consideration. So if you have an element listed in the elements array and that element is inside one with the ignoreClass specified, then it will still be processed. That is because you have explicitly told MathJax to process that element by including it in the elements array. For example, consider the following:
<!DOCTYPE html>
<html>
<head>
<title>Check elements array and tex2jax_ignore/skipTags</title>
<script type="text/x-mathjax-config">
MathJax.Hub.Config({
elements: document.getElementsByClassName("math")
});
</script>
</head>
<body>
\(x+1\) not processed.
<hr>
<div class="tex2jax_ignore">
\(x+1\) not processed.
<div class="math">
\(x+1\) processed.
<div class="tex2jax_ignore">
\(x+1\) not processed.
</div>
<code>
\(x+1\) not processed.
</code>
</div>
</div>
<hr>
<div class="tex2jax_process">
\(x+1\) not processed.
<div class="math">
\(x+1\) processed.
<div class="tex2jax_ignore">
\(x+1\) not processed.
</div>
<code>
\(x+1\) not processed.
</code>
</div>
</div>
<hr>
<div>
\(x+1\) not processed.
<div class="math">
\(x+1\) processed.
<div class="tex2jax_ignore">
\(x+1\) not processed.
</div>
<code>
\(x+1\) not processed.
</code>
</div>
</div>
<hr>
<code>
\(x+1\) not processed.
<div class="math">
\(x+1\) processed.
<div class="tex2jax_ignore">
\(x+1\) not processed.
</div>
<code>
\(x+1\) not processed.
</code>
</div>
</code>
</body>
</html>
In this example, each of the <div> elements with class="math" will be processed, regardless of the container element's class or tag. But within the math <div> the tex2jax_ignore and <code> blocks will be ignored, as usual.
So this is not a bug, though it may not be the behavior that you would like.
I hope that clarifies the situation.
Davide