I've been using WP for quite some time and have recently had a major issue with hyperlinks being stripped from posts. I'm not sure if the scheduling feature is doing it or not, but I'm forced to write all posts in Evernote, copy and paste into my blog editor, wait for it to go live, go back to Evernote, copy and paste the same code into my editor again and update. After that all links remain.
After the stripping the phrase that should have been hyperlinked look like this example. It also removes Amazon ad code and YouTube video code in their entirety.
I don't know if this makes any difference, but I never use the visual editor, only the html editor.
I have a sandbox site with the same template and the two latest plugins added to my primary site: Disqus and Shareaholic. The sandbox site is not stripping out the links. I have no other new plugins. I updated to 3.5 about 3 weeks or so ago (I think).
The only major plugin difference between the two sites is Jetpack is activated on my primary site and not activated on my sandbox site.