Turns out it was the cables LOL.
I had mini display ports on my ASUS GTX680's. So I got mini display port to display port adapters to make them work on my R9Furys.
The problem is both cables and cards though, some cards must just not have been completely tolerant of the adapters, while one card was completely compatible. It's enough to drive you crazy trying to figure that one out.
What finally clued me in was the last RMA. It was working fine, but the other card (one of the original 2 I purchased) was experiencing occasional drop outs from Eyefinity. I figured it was one of the very first production runs, it must have an issue too because the most recent RMA had zero problems. The most recent RMA went days without any drop out from Eyefinity. So I pulled the first card and was going to ship it back and then walla, the new card dropped out of Eyefinity, so at that point rather than ship anything back I bought new cables.
The new Displayport cables were twice as thick as the displayport to mini-displayport cables and of course don't need an adapter to go back to normal displayport.
It's been two weeks. Not a single drop out, no flickers, everything is working.
OK so, it's not all cable, the cards reacted differently on the same cables. However, it was the cables, I am sure had I swapped them out from the start I'd have fixed the problem.
Arghhhh...