Hi
I do apologise for the troubles you're having with the new software, the Warn for Duplicate bug is set to be fixed on our next release which is set to come out in the next few weeks. I suggest to keep an eye out on the AccountRight Blog.
As for your issues with pre-filling information, I suggest having a look over this support note: Working with In Tray documents
In short, when the document has been loaded into the software it will attempt to use OCR to read the information from the PDF to pre-fill the fields as it can. This may not always work for some documents due to the nature of some of the documents out there as the OCR technology is looking for the most common places for the information to be kept.
With that said, sometimes blurry or low resolution text on the documents being uploaded may not be able to be picked up and so it can't pre-fill in the fields. You can use the information on the above support note to look into the details on this.