Sorry to post here with no real solution, but I've experienced something similar to this.
In my case, I had a fully functional Zephyr that had been Jtagged for months, before the ROL decided to pretty much quit functioning. It did nothing but turn the system on and off. Nothing else worked with it, including controller syncing. I found it very odd that it would turn the system on and off, but at the same time, display no lights at all. Swapping ROL boards did nothing either.
Checked soldering, all looked fine. But of course I re-soldered to be sure . After re-soldering, voila! It worked right away........for one boot >.> as soon as I shut it down though, the next few reboots varied between lights on and off. It was the oddest thing I had seen yet come from a Jtag.
Like I said, I'm sorry for no real solution, but I guess if I learned anything from what happened, it had something to do with the soldering. I can't imagine what exactly changed during re-soldering, but it obviously did something.