The smallFonts plugin is broken in 3.6c, at least in certain browsers such as FIrefox 3.5.3 on Linux. It includes statements like
jsMath.styles['.typeset .size0']['font-size'] = '70%';
which throws an error because jsMath.styles['.typeset .size0'] is not yet defined. At least in the above-mentioned browser, the error prevents the rest of the smallFonts.js script from executing, so the smallFonts plugin has no effect.