I am seeing the same things, but mine is a little worse because it is also added <script> tags before the Shortcode. which shouldnt be there and is messing up the formatting on my site. This only happens with the 1.8.6 plugin version.
For the <p>
tags issue look at this:
http://wordpress.org/support/topic/plugin-shortcodes-ui-tags-being-stripped-from-shortcodes-ui?replies=1#post-3305992
as for the script being added … I have no idea what that is and i can’t replicate so i guess its something in your setup.
more details will help.
For the <p> </p> tag issue I have tested all the options in the “Fix AutoP filter:” feature. None of them make a difference and it is still puts the <p> tags around my short codes. for example check out http://samplesite2.optimized-marketing.com/ the Phone number and hours in the header as well as the word “Massachusetts” at the bottom of the page and it the footer are all shortcodes and all have <p> tags around them in the source code. The code I am entering into the shortcode HTML section is just text (No Html markup or anything special) with the ShortCode Type: Simple Snippet.
I am using Genesis Themes with the Venture Child Theme on this site. It also is happening on a different Child Theme.
WP version 3.4.2
I don’t see the <script> portion any more. So we can ignore that for now.