I've recently updated a site to use WordPress 3.5 with the latest version of Shortcodes UI (1.9) and it's currently causing an issue with the formatting (WPautoP filter).
This was identified a week ago in another thread:
http://wordpress.org/support/topic/v186-issue-adding-p-p-with-simple-snippets?replies=3 (apparently resolved for version 1.8.6).
When updating, I also re-saved the settings (otherwise the shortcodes don't kick in properly).
What's strange is that all existing shortcodes keep their formatting, however any new ones lose formatting. Hopefully, this may be a clue?
Would be great to see this plugin working properly again! Keep up the great work. It's really appreciated. :)