I have the same exact problem with my quick books premiere edition 2016. 

I have to scan everything twice in order for it to save on an invoice or a bill. I tried dragging the file from the desktop into QB and QB shuts down when I attempt this. 

When I called this in, two people could not explain or help so they sent me here. 

The sample file does not have this issue, only my main file does. 

I downloaded File Doctor and it found no issues. 

I ran the repair option instead of uninstalling QB. I haven't tried uninstalling, then installing again yet. 

This is very frustrating and time consuming to have to scan every document twice!