I recently had a WordPress theme where the image captions would not be formatted. I wanted the standard grey box with text below the image but it was looking like the caption text was just floating in the middle of the page. I was able to get the formatting corrected by adding some code to my css file but that resulted in making all captioned images left align. I finally got it correct by adding this code to the css file.
Since updating to Shortcodes Ultimate 4.6.2, my spoilers, tabs, and accordions would no longer open, close or display properly. I tried disabling all plugins except for Shortcodes Ultimate but that did not help. The culprit ended up being jquery. My theme was referencing an older version of jquery that is no longer supported by Shortcodes Ultimate. I was able to update it with the plugin jQuery Updater (http://www.ramoonus.nl/webdesign/wordpress/jquery-updater/) so that it will always be up to date going forward.
Also, updating your Shortcodes Ultimate may force you to add su_ to every shortcode to be able to still work correctly. I recommend using the Search & Replace plugin (http://wordpress.org/plugins/search-and-replace/) and doing it on the following list of shortcodes (not complete depending on the codes you use). Finally, remember to always backup your custom CSS in the Shortcodes Ultimate plugin before updating it.