FYI, I had the same problem, and yes, Enter metadata was enabled. I don’t recall that I had checked that box before. I wonder if it is checked automatically when doing the update from 3 to 4.
On the other side, I struggled a bit to figure out that the INBOX path has changed with Vers.4, so it might be possible I checked it trying to overcome the problem with PDF not showing up in the new Inbox. It might be worth mentioning in your upgrade instructions that the Inbox-path has changed and the scanner software needs to be told manually.
ScanSnap ix1500 and ScanSnap Home. I installed DT4 without removing DT3, as per upgrade instruction. After the upgrade ScanSnap Home was still pointing to the DT3 Inbox. But that is what to expect. But that the DT4-Inbox path has changed was not expected. That’s where my confusion started.
It is not recommended to scan directly into the Global Inbox’s. See the in & Out > Going Paperless (Other Options) section of the built-in Help and manual for the recommended setup.