If you are comfortable with SQL and have access to the ManagementReporter database, I can give you a hint on this with the latest releases of MR:
-You need to insert the folder information from the original ManagementReporter.reporting.ControlFolder table.
-The reports are assigned to the folder in the reporting.ControlReport table. The folder is stored in the FolderID column. (I was able to do this with UPDATE scripts where I read in the data form the original ManagementReporter database.)
[I have only had to complete this process once for a client so I am not comfortable releasing any actual scripts. It was very fast and easy to do once I found the data. ]
Once I got the folders inserted and the reports updated to the FolderID, I confirmed I could see them properly represented in Report Designer.
[If you don't have the original ManagementReporter database, you could create the missing folders and then update the FolderID based on the newly created folders you see in the ManagementReporter.reporting.ControlFolder table.]
