This usually is related to the volume of folders and or reports that are in your Salesforce org. Use the following steps to change how reports/folders are displayed on the report scheduler:
- Go to the tab "Scheduler Settings"
- Go the field labeled "Show Report Folder as"
- Select "Picklist"
Once you've completed these steps, create a NEW Scheduled Report. You should be able to find the report/folder that had been missing.