This is related to the many permalink freakout posts I'm seeing here. I'm going to attempt to outline my 4 days of note-taking to see if someone else has an idea of how to deal with this.
Here are the facts :
-- Both 2.5 and 2.5.1 are having permalink issues on only ONE of my many WP sites, almost all on Dreamhost; this particular site is on a different DH server from the others which work just fine after upgrade to both 2.5 and 2.5.1.
-- After upgrade, nearly all permalinks, which remained set to Day/Name (domain.com/2008/06/06/sample-post/), failed to work, defaulting to index.php and not using page.php. Not only top-level pages failed, but all sub/childpages in the main menu. These pages are linked via an unordered list that is hard-coded into the header template (i.e. "/permalink" or "/parent/permalink").
-- Any wp_list_categories instances were completely non-functional.
-- I have verified the .htaccess file and site index.php (at root level but referring to the site which is in a subdirectory). WP writes perfectly to it. I also tried going back to having full site URL reflect the subdirectory and no go.
-- I installed AskApache RewriteRules Viewer 3.0 and looked at this info and all appears good to me (as far as mod_rewrite being active, etc.).
-- I then switched to default permalinks and this works but of course all internal links are now non-functional.
-- I tried changing to default theme and voilà, original, Day/Name permalinks work, so I carefully compared header/footer code to be sure my theme doesn't have something questionable (it worked perfectly up to now) and cannot find any reason why it and the page.php are not working. I have no sidebar widgets nor dynamic widgets code in sidebar file.
-- I tried shutting off all plugins and reactiving one by one. Doesn't change anything.
-- After the upgrade, one page, which used a custom template, continued to work, including its childpages that display as a submenu on the page. When I cloned this page template and attempted to use it for other pages that were not working, it wouldn't function at all, defaulting to index.php. And when I click on a page to go there, even though it defaults to index.php, it shows the correct permalink (maybe this is normal?).
-- I have temporarily created a completely separate template for all parent pages using Improved Include plugin, which works, however I am stuck with having to create an awful lot of custom templates!
-- I am suspicious that there are issues with the upgrade and the database; I've taken a peek at it and nothing has jumped out at me but I'm not an expert in MySQL. I had a previous upgrade, to 2.3 I think, cause many problems with page becoming posts, which I fixed manually without any real problems following that incident, but I'm wondering if something else went awry that I'm not aware of...
-- Weirdness note : At one point, one of the pages showed a "Page slug" option down with the "Page template" and "Parent page" options in WP Admin but then it went away after logout/login.
Suggestions? I would reinstall but I'm concerned that if the DB is the problem, I'll just be duplicating the mess. Help!