FYI; the problem persists when using the default template.
I posted about this, with a less then ideal subject, recently as well:
http://wordpress.org/support/topic/352438
Unfortunately, I can’t look into it too deeply where I am. I’ll watch your thread too and if there is a resolution, I’ll let you know.
I’ve setup a rewrite log and don’t really see anything going on. The server config hasn’t changed since upgrade nor has the .htaccess file that’s sitting in the root directory.
Not sure what to make of it. I really want it to work but it’s really slowing my development down. I’m going to give it another night and then probably try it on a production staging machine.
Really no one else has had this problem after upgrading to 2.9?
Alright, this is embarrassing but my build system reverted my Apache config, disabling mod_rewrite.
For you googlers out there, make sure you have this line un-commented:
LoadModule rewrite_module modules/mod_rewrite.so
Don’t forget, double check your <Directory> directives for allowing .htaccess.
Also, double check that your mod_rewrite is “sane” before doing anything. Try this method:
http://www.webune.com/forums/how-to-test-check-if-mod-rewrite-is-enabled-t40.html
Good Luck!