I have fixed this little issue but I haven't released a final release of the plugin because there is another change in there.
If you download: http://downloads.wordpress.org/plugin/wordpress-bootstrap-css.zip
You'll have the latest code. It has 2 changes:
- a fix for this particular issue you have highlighted.
- a large optimization for including CSS so that it isn't calculated on every page load, but instead calculated once and saved.
If you download this version and you experience a problem with including the files you need, please let me know. I believe it's working and stable, but any testing of this would be appreciated.