When using QuestyCaptcha the form appears when the user has done changes and is on the same page (edit). The user is not aware that a captcha must be filled. Moving the Captcha to the bottom of the page or highlight it by css would change the problem.
Topic on Extension talk:ConfirmEdit
I agree, this is causing confusion for our users on the Create Account page, as well as the Edit page as described above.
The issues is known but the solution is not trivial, because MediaWiki can't always know beforehand whether the edit will need a captcha (e.g. whether it will add an URL). In recent versions, Special:UserLogin shows the captcha from the start when required for registering.