Hi,
Depending on when you downloaded 2.3.9.7, you may not have the most recent files. There were some bugs with the new uploader which were fixed after 2.3.9.7 was initially released. The 2.3.9.7 release was patched but you'll have to download it again and replace the changed files in your installation. Go to the codeplex site to download the release and to view the addtional notes on which files were patched.
Also, make sure you used the new web.config file from the release. Copy any of your own customizations to the new file and use it, don't continue to use your old one.
HTH,
Joe D.