I think it is a driver or cable issue. I too have had days of trouble getting the wugfresh nexus toolkit to work on both the 2012 and the 2013 nexus 7. So here are my hints that could help.
1. Be sure you are using the usb cable that came with the Asus charger! The other cables I used worked for everything else but not with the toolkit. Wasted a lot of time here till I discovered this.
2. The universal drivers did not work for me. The signed Samsung drivers worked. Try them.
**Possible reason why the universal drivers didn't work for me:
The Samsung drivers do not appear as installed on my Windows 7 64 bit laptop. I discovered this when I went to install the Samsung adb drivers (using the toolkit) and the install process told me they were already installed - even though I had removed all usb drivers as instructed. The Samsung drivers did not display as being installed in the 2 screens the toolkit asks you to check for uninstalling. So I think their hidden presence might conflict with the universal drivers because they are not uninstalled before installing the universal drivers. Don't know.