Ok, I managed to fix it myself. It seemed that some essential MathJax settings were placed after the actual MathJax script. What the settings actually did was to recognise the single dollar as a legitimate method of inserting inline TeX (and not just the \.( \.) without the dots). So whenever a post used the dollar method for inserting TeX instead of the TeX button, the TeX was not rendered.
I've tested it about a dozen times and the fix seems to work. @Trimok please tell me if you continue to encounter the bug. If not, I'll mark this as status-completed.