I don't use Jmol.js often or the applet, so the problem may be trivial.
With the Jmol extension for MediaWiki, checkboxes don't seem to work.

See for example http://wiki.jmol.org/index.php/Uploaded_XYZ_File

Does someone know what's wrong with the generated HTML ?

<p><!-- Jmol --><script language='Javascript' type='text/javascript'>jmolCheckBrowser('popup', '/extensions/Jmol/browsercheck', 'onClick');jmolSetAppletColor('orange');jmolApplet(200, 'load /images/Chair.xyz; ');jmolBr();</script>

</p><p><br />
<!-- Jmol --><script language='Javascript' type='text/javascript'>

jmolCheckbox('select all; color red','select all; color blue','testing jmolCheckbox, should color red/blue',false);