Online Backup for WordPress 3.0.4
Under General Settings > Filesystem excludes: both "Exclude plugins" and "Exclude themes" was selected. Save Settings was clicked.
The Activity log says:
Folder /mysite.com/wp-content/plugins/wponlinebackup/tmp was excluded: Temporary backup directory
Folder /mysite.com/wp-content/themes was excluded: Themes directory
Folder /mysite.com/wp-content/backups was excluded: Local backups directory
Note that it doesn't say:
Folder /mysite.com/wp-content/plugins/ was excluded
I checked the backup zipped file that I downloaded and the plugin folders and files were still there.