Could you post a picture with the backlight on both of the chips? I had one that didn't look bridged but looked almost fuzzy, and its on the way to the doctor currently.
My second EtD was also having problems, but I was able to reflow one side of the small chip (with a lot pen flux and a quick solder sucker to fix the bridge I caused). It went to working immediately.
The way mine appears to work is that if the green light on the magjack comes on then you have a link to whatever you are connected to. Once you turn on your E1.31 output then the yellow goes solid where it only randomly blinked before. It sounds like you are close but the pic isn't recognizing the broadcast data. I would think the most likely cause would be an improperly flashed PIC, but it sounds like you have programmed it several times with not much different results. The next most likely cause would be a bridge on the Comm chip or the PIC which is grounding or sending the data to an unintended location which may be why universe 2 is acting strange.
Also have you checked the voltages on the 8 and 50MHz clocks? There was a post around here recently that had the voltages and a link to the spec sheet that showed what the pin numbers where. I would imagine either of those failing would also cause odd behavior.
Edit Found it. You are not allowed to view links.
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