When I drag a folder to the window, only one of the subfolders get verified. Why?

When you drag a folder onto Checkpoint, it will scan the folder for Media Hash Lists (.mhl files). MHL's are created by copy software like Hedge / SilverStack and others. The .mhl contains references to the files that got transferred and their calculated checksums. So only the files that end up in the .mhl can get verified.

Checkpoint can also create MHLs. Drag a folder without any .mhls onto the dropzone and press "Create MHL."