A few things are still unclear to me. I presume you are using the ZED with FMCOMMS1, I don't know to much about your tool version, I would recommend to use Vivado 2013.4.
Another misty spot to me, how do you create your system.bit file. Currently we have a several, different options in the wiki page, please use the one with Vivado, if it's possible.
Try to make sure that, the Digilent plugin for USB-JTAG is installed, and you can access the JTAG chain. You can verify this by simply open up a Hardware Manager on Vivado, and trying to connect to the board, while it's powered on.
Istvan