The reason this is happening is due to a Salesforce limitations that is restricting our Report Scheduler from displaying all of your Report Folders. Once you make this change, you'll notice a new step is required when scheduling your reports. You will have to select the Report Folder Name first, then you will select the name of your report. 

Go to the Scheduler Settings tab, then make an update to the field named "Show Report Folders as". Change selected value from "Auto Lookup to "Picklist"