It sounds like you are having issues getting Paperless to work with your ScanSnap. Let us ask you some questions to better figure out what is going on.

When you initiate a scan by pressing the "Scan" button in Paperless what happens? (should scan all documents as one item.)

When you initiate a scan by pressing the Scan Multi button in Paperless what happens (should scan each page to a new file.)

If you look at the Scan to Paperless Multiple profile in Fujitsu's Scan Snap Manager (SSM), under File Option, press the Option... button, it should look like this:

the Scan Multi profile should look as above. If not, change the setting.