Same problem here…
I can upload the files, insert them in the posts and all… BUT if I want to see the photo on the blog I have to manually upload it to the /wp-content/uploads folder (I use FileZilla) because the files do not appear to be in the folder (or anywhere else) after I uploaded them from the WP Dashboard Media Gallery thing.
And I can never see the Thumbnails on the Media Gallery either…
I only have Askimet and WP-Stats as Plug-ins. I doubt any of those can be the problem. As I’ve always had them and this thumbnails/photos problem only showed up with the latest WP package upgrade.
I don’t think having the photos in the theme folder is a smart thing to do. What if one day I decide to change theme? I’d have to move them all, change the links in the posts…???
For now, I’m using the FileZilla/external FTP upload trick to actually have the photos in the uploads folder as they should be.