I have four blogs working together on one install. I just upgraded from 4.1 to 4.2 rc1 I've been doing a lot of design work and having to rebuild quite frequently.
I just encountered a problem that I'm only given two options on the publishing screen. All Files or Indexes Only. Even when I pick All Files it only publishes indexes.
zach

What do you see in the publishing option for your archive templates?
I'm getting partial rebuilds as well. I can see all the options in the rebuild dialogue but many pages do not rebuild (see my problem here: http://forums.movabletype.org/2008/06/internal-caching-system-interf.html)
The Publishing option only shows
ALL FILES ONLY INDEXES
but publishing only give me indexes even choosing all files.
I abandoned that installation and created a fresh beta install and have now upgraded to rc4. i don't have this issue any longer. I still have search issues, that you filed as a bug. Thanks Fumiaki.