I've created a packaged report and although it is shown as scheduled, I can't find the package in the folders.
I had this problem before and deleted the app files and re-installed; however, I'm moving the scheduler into production and this isn't a viable solution.
Go to Tools - System Tools and Validate folder heirarchy. If this doesn't work, log a call with the helpdesk and they will retrieve it for you. When I had the problem, they advised me to ensure that I either increase my polling interval, or switch off the scheduling service when I am making changes. That way the application's "Save" action does not clash with the scheduling service's "Save" action. Apparently, under these conditions, the service gets priority.
I don't think you'd need to uninstall, you can delete the ReportDeskLive file and that will blow it away...
did you maybe delete folders? If you delete a folder, the reports in the folder disappear, but you can recreate teh folder with the same name, and like magic, the reports will be in it (may have been fixed in latest versions)