Sorry missed that out. Its the Inno3D GTX 560. I guess having water in your computer really does make you worry a bit more. Since the case is so small, I don't have much of an option to move the GPU/tubing away from each other. Although I can jam a few heat resistant wires between the GPU/tubing.
I need to run those 'burn-in' tests as I don't want to find out later that my hardware is faulty. Is it safe? Has anyone actually had a tiny case and ended up resting water tubes on other components? I'm still not sure :O
Neat - I only just squeezed one of those coolers into a Silverstone SG01 Evolution, and I imagine thats got loads more space your itx case.
In response to your original question - I wouldn't worry about it, the components are never going to get higher than 80-90C in the worst case and the tubes are water cooled anyway