Theme/Plug In conflict?

I’m wondering if the latest issue I’m experiencing is a theme/plugin conflict? I’ve used the TinyMCE editor on all my other sites, which are based on a child theme of Twenty Eleven, and it’s working fine there. But it doesn’t seem to work properly on this site. A couple of issues I’ve noticed (there may be others I haven’t found yet):

1) The second bar of menu items does not appear in the editor. I can’t get them to show up no matter what I do.
2) When I try to italicize a line of text, it puts an <em> tag around it instead of the <i> tag, and the resulting tag looks very weird.

Do you think this is a conflict with the theme? If so, is there another advanced text editing plugin you recommend?