Along with upgrading to 4.2, I've recently added some new templates to a blog and changed the archive mappings to point to these templates. After making the change I noticed each of the archive types that I added (category, monthly) vanished from the publish pop-up box. Only "indexes" and "page templates" remain as options. And "all files" does not rebuild the archives that are missing.
I can still publish normally from the templates section, but some of the blog's authors are comfortable with the pop-up box, so I'd like to return the templates to that box.
Thanks!
Reported on Movable Type 4.2

How does your archive template configuration compare to this? http://www.codemonkeyramblings.com/files/screenshots/mapping.png That's how my individual archives are set up, but the same rule should apply to any archive templates you have.
I have a different path configuration of course, but I definitely have the check box next to "entry" as in your screenshot. And "statically (by default) selected.
But as I mentioned in the first post, there was a few minutes between when I unchecked the old templates and checked the new template as the default. Maybe it got broken at that point?