I just sent this in an email to Ryan, but I thought I should probably post it here too, just in case anyone else is seeing it.
http://www.randomthink.net/dump_env.html is a sample of my problem output. My issue is notably different from the others I've seen on the boards, in that not only do my permalinks work fine, but now WP is catching odd random other requests, even when the files/folders exist.
http://www.randomthink.net/archives/2005/12/30/wordpress-20/ - works fine, comments are fine too. There is a /wordpress folder under randomthink.net where I house the files, so I'm a little surprised that a slug with wordpress in it was working okay. I did update to those two files that Ryan posted - the functions-post and classes, I believe, including rev 3396 of classes, so that might be fixing that.
http://www.randomthink.net/tests/ - this isn't a WP page or anything, but simply a directory with some html files and whatnot, and it loads fine.
http://www.randomthink.net/gallery/ - my G2 install, works fine.
http://www.randomthink.net/awstats/ - my awstats install. This one doesn't work right. WP intercepts the request and gives me a pretty WP 404. I've tried adding index.php to the request (shown in the dump_env above), and it doesn't work then either. It works fine if I turn on verbose rewrites with Ryan's plugin.
http://www.randomthink.net/awstats/icon/clock/hr1.png - a file deep within my awstats install path. Doesn't work, is caught by WP. Technically, the icon folder under there is a symlink, but that option is on in Apache, and it works fine if I'm using verbose rewrites.
http://www.randomthink.net/misc/ - a directory that's closed to open viewing, with no index file. It gets intercepted by WP. However, if I put an index file in there (be it .html or .php), I get that file, so it's a half-works.
http://www.randomthink.net/misc/wow/ - a directory that's explicitly open to everyone. Works fine, regardless of index existing there or not.
It's seems like a random crapshoot as to whether or not folders that are at the same level as my WP index.php file (which is now the root of my site) work or not.
I'm fairly certain that this is due to the .htaccess file handing everything off to WP that fails the -f and -d tests. However, some of those things shouldn't be failing that test, but seem to be, since WP gets the request.
I'm a DreamHost customer, and they've asked that we run PHP as a CGI. I've even noticed comments in some of the WP code mentioning adjustments put in place for that. I'm not sure if that could be causing some of the problems.
Any insight you could offer would be most appreciated. I'm really comfortable in and around a shell, as well as with PHP, so if there's anything that needs to be altered or adjusted, let me know and I'll get it in rather quickly.
For now, if I turn on Ryan's rewrite.php plugin, it just writes out the verbose rewrites and all is well. However, I'm going to keep that off for the moment so you can go poke at things, should you so desire.
As an aside, I've noticed that sometimes I can turn on the verbose rewrites, pull up my awstats page, then turn the verbose rewrites back off and continue to look at my stats, including a full refresh, so long as I don't close my browser. That one could be that my awstats are guarded with basic auth, and something about being authenticated might be making the request go through past the -f and -d checks. That doesn't make sense, but not much else has made sense with this issue so far, so I'm not surprised.
Thanks again for any help and/or insight you can offer.