Moodle 2.7 used MathJax version 2.3 as the default. Moodle 2.9 I believe switched to MathJax 2.5. The MathJax version may be changed by changing the settings for the MathJax filter. Yo u probably did this if you installed a local copy of MathJax.
If you are using MathJax 2.5 or later, there is a new display mode called Fast HTML. This mode is meant to load very quickly, but it is lower quality and does not do well in some situations. From what I see above this may be the mode you are using. You change it by right clicking an expression in order to open a MathJax context menu and then choosing Math Settings -> Math Renderer -> HTML-CSS from the submenu. If that does not work, try SVG.
If you try the TeX notation filter, you should make sure MathJax is off. Otherwise it may override the TeX notation filter.