I’ve run a Scansnap S3100i for many years, attached to a headless Mac Mini which is set up as a server. Documents put through the scanner are scanned, converted to searchable PDF, and dumped into a folder shared over the LAN. Scanning is thus a no-intervention process…
The earlier version so Scansnap Managers just dealt with any errors encountered with the OCR step - I believe it just ignored them or logged them. However, the later versions (as from Catlinea, I believe) now put up errors in a modal alert message, so the whole thing gets blocked until the message is cleared by a user. Does anyone know of a way of suppressing these alerts, so that errors are either ignored or logged, rather than needing user intervention?
Check the permissions in:
System Preferences > Security & Privacy
You might have to approve the application at the borrow of the General tap
Then the Privacy tab and check the boxes where needed.
Thanks for the suggestion. I’m not sure that I entirely understand the bit about approving " the application at the borrow of the General tap (I assume that means the bottom of the General tab), but there is nothing relevant on that tab, and no outstanding approvals under the Privacy tab, either, so I don’t think that problem lies there.
I am slightly puzzled to note that there is no entry for ScanSnap Manager in the Notifications settings, but I assume that the authors have chosen to avoid that mechanism entirely. To me that would be the lazy way of programming things, and I don’t understand why these things should be a problem now when they used not to be - either there is some configuration item that I’ve missed, or the authors have chosen to spoil something that used to work really well …
Indeed Scansnap has become a big disappointment. Their hardware is great but the software is a complete mess. Like anyone else they are trying to push it to the cloud. Frankly thats the last thing I want to do with the things I scan put them on some one else their cloud…
I suggest to reinstall the Scansnap software can go trough the steps to setup. When you do the installation it might well ask you to approve the installation of the software in System Preferences > Security & Privacy. At the bottom of the General tap it will show a message to approve the installation of this software by this developer.
Next is to verify again if you need to check more boxes under the Privacy tab.
Once the installation is successful you can tweak te settings to keep your scans local and make it function more or less the way it used to be.
Its a pain 
A very belated update - my apologies for the delay.
I updated the OS on the Mac mini in question to Big Sur, and reinstalled the latest version of the Scansnap Manager software, and my problem seems to have gone away. The software isn’t quite the same as it used to be when I first bought my ScanSnap several years ago (and I can’t quite put my finger on what it’s doing differently) but it has stopped being obstructive, and is near enough to the way it was to be perfectly usable again.
Fujitsu have taken a lot of stick for their original cockups with this software and for making old devices pretty unusable for a while - and I added my own voice to those protests. That said, I have to take my hat off to them for taking positive action to fixing the problem - reviving ScanSnap Manager, bringing it up to date, and converting it to 64-Bit format, and for continuing to provide up-to-date software for hardware that is old enough that most manufacturers would simply declare it obsolete and refuse to support it. On top of that, one must acknowledge the quality of their hardware that still runs faultlessly after all these years. For all that they deserve a big round of applause.