Something that you might try, instead of using the v3 Beta of the stand alone programming software, try it with the version 1 from the Wiki. I had the exact same issue going on and sent my EtD to another user and they reflashed with v1 (I used the v3 beta) and it started working.
I am the one that created the chip database file for the v3 beta and I'm thinking that it may not be working correctly for the chip on the EtD. If you find out that flashing with the v1 works, please let us know and I'll talk to Rick about removing the database file from the Wiki until we can sort out what went wrong.
When I was flashing the EtD with v3, I received no errors and everything looked like it was working (LEDs on the MagJack doing what they should, etc.). So there may just be something wrong in the database entry.
I hope this gets you going in the right direction!