The same issue comes with Brother ADS-3100
After trying for days and hours on the phone with IT and Dentrix I have found that this is a Dentrix issue. The newer scanners (like the ADS-3300W) are not working well with Dentrix. Something about Dentrix not updating their system and therefore not being compatible with the newer TWAIN drivers in the scanners. TWAIN driver is what is needed to scan duplex, ID cards w/o a background, etc...
You should be able to Duplex Scann with the Brothers ADS-3300W scanner, it might be a twain instilation issue. I was able to Duplex Scan into doc center with out issue. Have you tried Unistalling and reinstalling the twain?
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