Everything Uploading to Blogs.dir

Hi, I’ve got a multi-site with Buddypress and bbPress. Lately, it seems like all new directories or uploads are going to the blogs.dir/1/files folder by default. For example, I tried to install a new plugin by using the WordPress plugins>add new>upload from zip method. However, it failed because it was trying to create the plugin folder under blogs.dir. What is causing this? (If you want my domain name, please advise how I can get it to you confidentially.)