I have raised an RMA request for my 295x2, GPU2 is still hitting 75C (and throttling) within 3 minutes of playing a game despite upgrading the case fans and fiddling with the rad position.
I was playing Crysis 2 at 1440p yesterday (Ultra/DX11). With the Rivatuna OSD I could see GPU2 throttling down to 750Mhz at times!
They said they need to test it before they can replace it, which I understand.
I'm concerned they test faulty components in open systems though (to make swapping things in and out quickly, whilst testing) and it GPU2 might not overheat in that sort of environment so I made the point that I already beefed up my case fans to eliminate airflow/environment issues.
I believe your cooling has genuine issues. My GPU2 is running cooler than the GPU1 by 6C constantly. So something else might be the case with yours if they have the same plumbing.
However, have you tried to put the rad on outside the case and see if it continues to behave like that?