I'm actually using 3.0.1, but same problem with 3.0.
When I input a manual excerpt, it breaks the page (the loop stops and no other posts are displayed nor the footer).
When the excerpt is constructed automatically, the shortcodes are displayed (shortcodes for NGGallery and Flash-Video-Player).
I'm using WP_Query to retrieve the custom post types. Just <?php the_excerpt(); ?> to display the excerpts. When I use <?php the_content(); ?> though, the shortcodes are also displayed.
I have no idea what could be causing this... I've even tried a new function in the theme functions to definitely remove shortcodes from the excerpt and it doesn't work.
Any ideas? Thank you!