Okay -- I think I found out what was wrong. When Valve moved things to the new style of their back-end, it looks like one file may have gotten missed. (?) Not sure on that. In my case, when I did the build of 6.0 independently of what they had done, my build was definitely missing a file. It's a file that only is used in the Steam version, specifically for achievements integration and so on, hence why I missed it in all the craziness.
Anyhow, you should see an in-Steam update now that should fix it and then all should be well. Let me know how it works for you!