Multi-Select Picklists Not Available in Salesforce Reporting Snapshots

As a workaround, create a Formula field for every picklist value to report on each selection.  The formula fields can then be mapped in the Reporting Snapshot creation.

For example, if the multi-select picklist field is called School, and the available values are Class 1, Class 2, and Class 3, and you want to see each time one of these options is selected, you'll need to create a Formula field for each option. The formulas would look like this:
 
Class 1:  IF(INCLUDES(School__c, "Class 1"), "Class 1","NA")
Class 2 : IF(INCLUDES(School__c, "Class 2"), "Class 2","NA")
Class 3 : IF(INCLUDES(School__c, "Class 3"), "Class 3","NA")