Okay, I've read about every topic and post I can find on this; time to be clear about my issue...
I'm running WP 2.8.4, Atahualpa theme with about 25 widgets. My hosting is through GoDaddy, who have been helpful throughout the troubleshooting process, but to no avail.
Here's the issue: When I upload using the WP interface (files like PDF or JPG), the files always go into /wp-uploads/2008/08/. No place else. When I use my blog editor, Zoundry Raven, it puts its picture files (and any others it uploads) into the appropriate year and month folders. Raven has never had trouble with making a new folder if it needed to. Raven uses XML-RPC protocols (xmlrpc.php inside WordPress) to facilitate uploads.
First important observation: The issue I'm seeing didn't begin until I upgraded from 2.7.x to 2.8, and has continued through to 2.8.4. I have used the auto-updater button on the Dashboard for these upgrades.
In my Miscellaneous Settings, I have "Store uploads in this folder" set to wp-content/uploads (no leading /), and this wasn't changed from 2.7.x to 2.8.4. The "Full URL path to files" box is empty. I have checked (and have always had checked) "Organize my uploads into month- and year-based folders". I do not track links' updates.
In a nutshell, I made no changes to file locations or file storage settings, and haven't done so for a year or more (back to WP 2.6.x). But the behavior of my WordPress blog certainly has changed. Raven has no trouble finding (or making) the directory.
Using some ideas from other, similar threads, I tried setting my Permissions (CHMOD) to 777 for /wp-contents and subfolders. However, GoDaddy doesn't allow that; 775 is the highest allowed. That should be fine though, as the only permission missing is for other users to write to the file structure, and nobody else needs this. (I'm the only user, besides admin who is also me, who needs to write anything to this blog's files.) Changing permissions didn't change anything; the integral media uploader in WP still goes to /uploads/2008/08/.
I reset my server permissions back to 755; I'm not comfortable with lower security, and in any case, this whole issue didn't exist before using WP 2.7.x at 755.
I checked with my IP hoster, and they made no changes about the time I upgraded that might have caused this behavior. GoDaddy has always been a stable platform for me. I think the odds are small this is a GoDaddy problem, since so many other WP users are seeing this problem in some form or other.
I tried unchecking the Organize function in Miscellaneous. This works as expected; that is, uploads then go into /wp-contents/uploads/ only. So I put that function back, and again, uploads go into /uploads/2008/08/ using the Media Uploader. This is true for either version of the native uploader.
I read where there might be a problem in the MySQL database on my server. I looked in the tables, the upload file location is shown as wp-content/uploads, as expected. I made no changes to the database.
I read in another thread that there might be a theme error which leaves out header, footer or both. I can see these items in the page source. I am not skilled in interpreting the javascript calls, though; there might be something there which is missing or bad. I don't find any other users of Atahualpa that are reporting similar issues.
Finally, I'm using Mozilla Firefox 3.x as my browser. I haven't looked for any issues through Firefox. I used Firefox well with WordPress in previous WP versions, no problems with uploads.
Somehow, it seems that WordPress 2.8.x is ignoring the "Organize my uploads into month- and year-based folders" option when the built-in Media Uploader is invoked. Coming into the file structure from a third-party program (Raven), which goes through XML-RPC via a PHP function, has no problems organizing my files.
I upload a lot of files each month, and I really need for this functionality to work again. Taking care of everything "by hand" is tedious, and based on previous versions of WP, is also unnecessary.
Another interesting observation: Unlike many other threads, I get no error messages, and I get no upload failures (in the sense that the file is missing, corrupted, etc.). The file is simply not where I expect it to be, and where I need/want it to be.
Anybody with ideas, I'm ready to try...