Can you share more about the site you're having these issues on? Please provide a link if possible. Also, what version of WordPress are you using? Does any of the behavior improve if you activate the Twenty Twelve theme temporarily?
Can you also provide a link to your site? Also, how did you install the update? Did you do the one-click auto update in your WordPress admin, or manually download the new files and install over FTP (or the manual .zip upload in your WP admin)?
My questions above for daigreen apply to your post as well, so check those out. Additionally, you said, <i>"All my mp3s were originally shortcoded with "audio" so now I have about a thousand audio files that show nothing but bare links."</i> Just to be completely clear, were these all using the WP audio player? If these shortcodes used another plugin, can you link to that plugin?
Thanks for your patience everyone, we appreciate the feedback and can get an update out to fix issues as soon as possible.