It possibly in data format error. Just experiment with the data in different types and formats, with ' ', without, with date() etc. I beleive if you decopmose every step of your load and every proccess that currently handled with script scenario you will be able to impress your own solution with this load.
As for duplicates, define which how would you use the data model? Do you need to see the rows in separate tables, or in one main containing data from two access databases? Try to draw a model you want to get for your task on paper. And what should you do to get this. And you will do the needed script in action. You can remove duplicates with different ways in QlikView, f.e. as I understand the duplicates are between 01/08/2010 to 03/06/2013? If it is so, just remove in load script just for start with where date < or > or beetween the dates, get the data and improve.