http://wordpress.org/extend/plugins/shortcodes-ultimate/
The plugin seems run the wpautop function or the the_content filter in a way that it is runs on other shortcodes which is opposite of the way WP processes shortcodes by default. The issue this causes is that extra line breaks and paragraph tags are inserted into the template output.
This would also negatively affect any shortcode based plugin, but would likely only noticeable on plugins that output significant amounts of HTML.
NOTE: This FAQ was written based on Shortcodes Ultimate 3.9.5