Why doesn DEVONthink Pro Office manage to change the ScanSnap settings?
In rare cases, the preferences file of the ScanSnap Manager application has the wrong read/write permissions. Simply close both ScanSnap Manager and DEVONthink Pro Office and delete the file ‘~/Library/Preferences/jp.co.pfu.ScanSnap.V10L10.plist’ (maybe with a different version number, depending on your ScanSnap Manager version). Then start both again and let DEVONthink fix the ScanSnap preferences. It would work now, you just may need to re-adjust the ScanSnap settings in ScanSnap Manager.