Hi, first allow me to say how awesome WordPress 3.5 and the 2012 theme are! Just amazing! Thanks to everyone on the WordPress team for what you do!
The problem: When WordPress is in its own folder, I'm unable to get more than two 2012 "child" themes for the new 3.5 install. I haven't had this problem until WordPress was in its own folder; I was able to employ several different child themes prior to this. There are no plugins activated. This behavior holds true for both my "scratch" site, at http://cook-my-catch.com, and a development site currently behind a firewall (and therefore unavailable for viewing--the point is, lightning is striking twice here, and this isn't a one-off occurrence).
This is a brand new, clean 3.5 install, using 2012 version 1.1 as a main theme, and multiple child themes, each using the 2012 theme as the parent.
The multisite set up is for subfolders.
Here's the URL of the scratch site, using the "Home" child theme for 2012:
Here's the URL of the scratch site using the "sites" child theme for 2012:
Here's the URL of the scratch site using "Test A" child theme for 2012--it is an exact duplicate of the "sites" child theme, only with the functions file removed (to make sure there were no conflicts)
Here's the URL of the scratch site using "Test B" child theme for 2012, an exact replica of the child theme that works in an earlier site, except, of course, that the style.css sheet was renamed. All else is the exactly the same.
To sum, it seems like when WordPress is in its own folder, there seems to be a limit of the number of child themes allowed--these scratch sites don't seem to "read" the css files. This wasn't happening to me in earlier versions of multisite testing for 3.5, when WordPress wasn't in its own folder.
Again, I want to thank the awesome team that is WordPress. What you do is nothing short of amazing. Thanks again.