I have exactly the same problem, mentioning this since Mystique 1.4 but sadly the problem did not solve until present day. As workaround I implemented the standard widget from Twitter. Works but it's ugly. Sometimes the Twitter timeline shows up, sometimes not, you will recognize the same on your page.
Actually running WP 3.0 Beta 1, Mystique theme 2.2.2 and the following plugins:
Contact Form 7, Find me on, Lightbox Plus, More Linke modifier, SI Captcha Anti-Spam, Syntax Highlighter Evolved, TinyMCE Advanced, WordPress Beta Tester, WordPress Media Flickr, WPTouch iPhone Theme.