Here is how I did a work around 

First I made a folder under my company data- (so I can always have a place to keep all the scans)

In my scanner option (default for mine)  I pick this folder and leave it as default, never change it. Even if I need to use another folder at a point in time I still leave it and just grab that file leave it, move it or copy it. Just makes things go faster)

So back to my process.  

I do everything exactly like before, and when I get on Make Deposit, I click on Attach Document.. (so far NO extra clicks)

I open my scanner (extra click 1)

Scan documents (Not an extra click)

It auto opens what I just scanned

I drag the top file into the attach document window (I don't care what it names it, I leave the default name) So not a click it's a drag and drop but lets call it one extra Step to be fair.. (2)

Save (not an extra step)  

So I guessed right, 2 extra Steps -  Done. It's working, I been doing it for a month now. 

Hope this help. If not let me know, I can do a video capture to show it.