After upgrading our old 1.0.1 installation to 1.1, none of our user’s home drives have any files and shared drives display all folder names (regardless of whether the user actually has rights to the folders) but they too have no contents. Has anyone else experienced this?

An overview of our setup:
Large install (Filr, MySQL, and Search appliances)
User Home Folders (Windows 2008R2 File Server), path listed in Active Directory
Shared Drives (Windows 2008R2 File Server), Permissions granted to individuals within an Active Directory group listed in both Share and NTFS permissions

Did anything significant change in 1.1 in regards to how Filr handles Windows permissions? Does anyone have any suggestions other than starting from scratch?