I figured out what the issue is, here. It turns out that there are a few "[Math Processing Errors]" earlier in the page, and that is throwing off MathJax's equation count, and so it is failing to reveal the last n equations (where n is the number of processing errors earlier on). The reason there are processing errors is that IE8 and below throw a run-time error when you try to set an elements style to a named color that it doesn't recognize. The way the default \color macro works is just to set the element's CSS color to the given name, and that is failing for some of the colors in the table of accepted colors. I believe that if you include the color extension (which implements the LaTeX-compatible \color command), the colors are handled through a lookup table, and so that should get rid of the processing errors in this case.
I'll look into having it handle the equation counts properly even when there are math processing errors, but it looks to me like the issue should not really be a show-stopper, as it is based on the presence of errors (and not TeX errors, but MathJax errors), not on the length of the page.
Davide