It appears that after finally getting a sucessful upgrade that we are unable to access the file manager. We get the error below (object not set to reference of object):

ActiveTabName: File Manager
RawURL: /Admin/FileManager.aspx
AbsoluteURL: /Default.aspx
UserAgent: Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.22 (KHTML, like Gecko) Chrome/25.0.1364.97 Safari/537.22
DefaultDataProvider: DotNetNuke.Data.SqlDataProvider, DotNetNuke.SqlDataProvider
ExceptionGUID: 86c667f4-fa7e-46b5-888f-05df05c53f35
InnerException: Object reference not set to an instance of an object.
FileName:
FileLineNumber: 0
FileColumnNumber: 0
Method: DotNetNuke.Services.FileSystem.FolderProvider.Instance
StackTrace:
Message: DotNetNuke.Services.Exceptions.ModuleLoadException: Object reference not set to an instance of an object. ---> System.NullReferenceException: Object reference not set to an instance of an object. at DotNetNuke.Services.FileSystem.FolderProvider.Instance(String friendlyName) at DotNetNuke.Services.FileSystem.FolderMappingInfo.get_ImageUrl() at DotNetNuke.Modules.Admin.FileManager.FileManager.PreloadFolderImages() at DotNetNuke.Modules.Admin.FileManager.FileManager.InitializeTree() at DotNetNuke.Modules.Admin.FileManager.FileManager.OnLoad(EventArgs e) --- End of inner exception stack trace ---

The thread got me semi pointed in the correct direction. I saw that there were no errors in the log on the upgrade, but copying over the HTML module code and dll from a working install seemed to fix the issue. How wonderfully odd...