This issue started for me after I added an Update Panel to the aspx page.
If the calendar extender is showing up weird, like with no background and is displayed no where near where it should be this could fix your problem. Take the original css from the control toolkit (AjaxControlToolkit\AjaxControlToolkit\Calendar\Calendar.css) and copy it into your css file in the application. No css modification is needed and you do not need to set the CssClass property to the control on the aspx page.
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