I have a similar issue here. I recently upgraded from WP 2.0.x to 2.6.0 and all images uploaded before the upgrade are missing from the Media Library…that is, after the upgrade, the media library was empty. I have since uploaded a number of images, and these all display as expected. But the pre-upgrade images, which are also contained in the wp-content/uploads directory (in their respective month and year based folders), refuse to show in the media library. The old images do, however, show in the appropriate posts. I even tried FTPing all images (no folders) into the uploads directory…and these still do not show, so it appears that they will only show if uploaded from the Write pages.
These files are set to be stored in the default directory, wp-content/uploads, and I have the full URL path set just for good measure. I know uploads in general have been buggy in 2.6…but this exact issue doesn’t seem so common.
Any suggestions?