Some amazon scripts that were built very bad don't include all of amazon products that Amazon.com has. This can lead to a drop in sales and some important items that should be listed, are not being included when you use such scripts. I only used the magnik free scripts and it has such problem. I checked AOM stores for such items and they were listed. so just to let you know.
Have never tried magnik script yest. Any good script would let you set your preferred Merchant ID, such as ALL, Featured, Amazon For it to list all items available you would need to select ALL. Likewise, some allow you to chose Condition, All, New, Used, etc. Have a look in the scripts code see if it lists "Merchant ID"