There have been a number of issues recently with how MathJax interacts with the editing preview code:
- MathJax preview bug
- MathJax not rendering in previews
- Problems with losing MathJax formatting previews while creating question or answer
and there are some older issues that have been in play for a while:
- MathJax preview broken when equations contain `\label`s
- MathJax makes preview flicker
- Only view MathJax in preview on button press
- Introducing a delay for updating the post preview box
- Would it be possible to not have the post-preview process ALL of the latex as you type?
Some of these are due to the code used by the preview editor not staying up-to-date with the new features of MathJax. Others are feature requests that have not been implemented.
I have written a user script that patches the editing code to resolve these issues by handling the new features more appropriately during editing, and by adding new interface checkboxes to control MathJax typesetting.
The new editing code is being evaluated by the StackExchange team, so it may not be necessary to use the user script in the long run, but you can give it a try now and see how it works for you. That would also help beta-test the changes.
EDIT 1: I've posted a new version of the user script that fixes some problems that were found during testing. If you have installed the script, you should get the new version.
EDIT 2: The changes from this user script (other than the checkboxes to control MathJax and error messages) are now available on math.se and meta.math.se, so this script is no longer needed unless you want the checkboxes.