I too was pulling my hair out with this same issue of the random page order and was finding very little on the issue. However, after some digging I found the following from Fujitsu:
http://www.fujitsu.com/global/support/products/computing/peripheral/scanners/scansnap/faq/hsierra004.html
The solution is upgrading to the latest ScanSnap Manager v6.3L70. I am on High Sierra 10.13.2 using a ScanSnap S1500, and this resolved my issue.
Hope this helps.