Follow these upgrade steps:
Delete the following folders from your server:
Delete all the *.php files from you root WP install EXCEPT:
Rename your plugins folder (so WP will think the plugins have been deactivated)
Upload FRESH versions of the latest 2.5.1. Be careful not to overwrite .htaccess or wp-config.php (shouldn't be a concern, files with that name do not normally reside in the distro).
Point your browser to http://path/to/wp/wp-admin/upgrade.php
Then rename your /plugins folder so WP can find those plugins. You should be fine. Normally it's okay to let existing files get overwritten, but sometimes servers burp and FTP programs hiccup. So I have found it saves time in the long run to just do it this way from jump street.