rikko101 - I would think you are trying to upload too many products at once and you are experiencing a time out, as qouted from the Readme.txt in EP...

TIMEOUTS: You may experience timeouts when adding/updating large numbers of products. If you have a large file that times out, you can use the "Split EP File" option. This will create multiple files containing a maximum of 300 records (default - you can change this in Admin). Thus, 1000 products will produce 4 files. These files are created in your /temp/ folder, from where you can upload each in turn after they have been split. If 300 is too many or too few for your circumstances, adjust it in Admin -> Configuration -> "Easy Populate".
gxjenkins - No EP standard will not change "Always Free Shipping" from no, to yes? you could use a SQL statement.

mafiasam - If you upload the Full-EP file with your stock qty in the v_products_quantity field this should update your stock qty.