Before scanning in DTPO1 I selected the group I wanted the scanned document to go in to and there it went. 
Before scanning in DTPO2 I select the group I want the scanned document to go in to but it always goes to the Inbox. 
Am I missing something obvious here, like a preference that needs changing, or is is a bug?
This is one of the things that changed with DT2: if the document is created outside of DT2 by an external application, it will always end up in the Inbox. Within DT2 it will go to the selected group.
It’s a feature then. 
So everything I scan with my ScanSnap will now need to be manually filed once it’s in DTPO2? Isn’t that a step backwards?
For some people, definitely yes. For other people, probably not. It’s a step forward in my opinion because it seemed like everything went in a different way, and there was no way to anticipate how things would behave. It was chaos, as Eric says.
One thing I’d like to see is the easy ability to create rules for sorting items sent into the Inbox. Like Rules in Mail. This can sort of be done with AppleScript, but it is quite difficult and not even remotely user-friendly.