Options System Snapshot / Excluded Folders page lists specific folders which must be ignored by the System Snapshot tool when taking and comparing snapshots.
The page offers a default list of Excluded Folders. Make sure that there is a check mark next to those you want to be ignored when working with the snapshots; remove the mark next to those which must be processed.
You can use the buttons under the list to add new Excluded Folders, modify existing ones or delete them. Please note that you don't have to delete a folder just to re-include it to the snapshots; instead, you can simply remove the check mark from the box next to it.
The button Default restores the default settings for this feature, including recovery of the items deleted by you and deletion of the ones added by you.