The only explanation I can quess is that some class in you theme might set vertical alignment of sup (and sub) to baseline - we had such a site wide bug in moodle.org some time ago caused by a css reset code http://tracker.moodle.org/browse/MDLSITE-681
For example classes .answer, .c1 or .text in theme css might do the job.
On my test sites TeX, AsciimathML and HTML work all well in Multiple Choice questions and answers. We had some discussions about drop down lists (IE won't show mathematical notations in drop down lists) but multiple choice answers seem to work fine. Is it possible to visit your site ( a demo course ) or see the source of that question / answer page?