On my site: http://www.weareecs.com, when clicking on events-calendar day (see november 6, 2008) the thickbox loads in the far bottom left of the page.
I am running the same site on ecs.inderhees.net and do not have the thickbox problems there.
Both sites are running WP 2.6 (verified all files in WordPress/wp-includes/js/thickbox are up to date) and neither have NextGen plugin that I see from the archives causes problems with thickbox.
Ideas why this positioning is off?