Just for the record, it's fixed again, yesterday I didn't really have time to experiment with this. To be exact, it's fixed only in Application Loader run directly by executing file Loader.exe. Application Loader started from inside DM still shows only third party apps.
Because, as mentioned by Midnightdraven above, Loader.exe is the core installer needed to add/remove applications, I'm not going to worry about DM.
http://img39.imageshack.us/img39/792...2009173823.png
The whole issue has something to do with Vendor.xml file, although the exact logic of the problem is not clear. You just need to keep deleting and restoring Vendor.xml until all the native apps are showing again. And even when the issue is fixed, it can reappear again after you decide to install or remove more applications.