Are we ever going to be able to write to the USB drive ?
Need some way to keep persistent data across executions ( structures, artwork, file accesses, playlists, logs ). The registry is OK for small items but even these get lost across Roku resets. You could make it at the user's discretion either by asking at mount time or at first write request. Another way would be to require the user to create a special folder ("Roku Data/Appname") and require all writes from the application to be to that folder's tree structure.
Not sure if this will happen or not, but in the mean time, you should be able to post data to your webserver and have it persist that way.
The data stored in the registry gets lost when you reset your device, this is intentional and isn't going to change. If you store data on your webserver, it will be persistent no matter what happens on the device and accessible to the user if they link from a new device or reset the existing device.