In includes/templates/Usercreate.php, there is a part that reads:
<?php $this->html( 'header' ); ?>
For some reason, the content put between the <section></section> tags does not inherit the CSS from its parents, with ugly consequences. For instance, when the ConfirmEdit extension is activated, and QuestyCaptcha is used, an input field is inserted between the <section></section> tags, which doesn't inherit CSS and thus looks different from the rest of the fields.
I've seen this bug in Chrome 33, Firefox 25 and Safari 6 (screens attached). This bug is probably not due to MediaWiki, but a short Google search didn't suggest that it's a browser issue either.
So anyway, rather than complicating ourselves too much, I suggest to simply change the section tags for divs.
Here is the Gerrit patch: https://gerrit.wikimedia.org/r/#/c/121291/