Uploaded images not showing up: WP 3.3.1, Genesis 1.8

I have been struggling with the Genesis/Enterprise to upload images on WP 3.3.1. This issue is related to the location of the uploads directory. It is now changed to wp-content/uploads/ but the uploads are still going to ‘wp-content/blogs.dir/11/files/…’. I have disabled all the plug-ins as well.

Upon searching this problem, some had resolved this issue by unchecking the option “Organize my uploads into month- and year-based folders”, but I do not see that option under ‘settings/media’ on my multi-site 3.3.1 installation.

Any help would be greatly appreciated.