I have five blogs running off the same database, and the same core install, with everything symlinked. This worked in 2.5.1 the occasional plugin couldn't deal with it but too bad.
I have an actual wp-content folder for each blog, with a symlink to the main install's plugins folder but an actual individual themes folder for each blog. This is better organized than tossing all my themes into the main install's themes. And besides who knows I might want to use the same theme on two blogs but that would cause trouble with naming folders if I didn't have them separated out.
OK, well, now it appears as if the new wordpress is only looking for themes in it's core install wp-content/themes folder, not in the ones I have configured for each blog because the only choices are classic or default--the ones in the install. Also, the only theme that shows a thumbnail or works is the default. I tried dragging a random theme into the main install's themes to see if it would show. WordPress made an entry for it, but no thumbnail, and when I tested it it had no formatting, and neither did classic.
I discovered a new file in the new install which the virtual blog folders did not have a symlink to: wp-load.php. So I made a new symlink in each virtual blog pointing to wp-load in the core install to match all the other symlinks. But that did not help with this problem.
I looked around at the config files: Here is the trick I use: My wp-config.php in the main installation is just this:
<?php require('local/wp-config.php'); ?>
assuming local will point to different places in different contexts and that seems to work.
In the root of each blog I have a folder called local with a config in it. In each config I hardcode ABSPATH to the root of each blog. I scanned quickly thru settings code and I just don't see why it's not looking for the themes where I want it to, and why they are all bad except default. Please help! I hate my blogs this way!