Yeah, a friend and myself have done some testing on that - he has a pair of 1.5gb 480's on water @ 850mhz - we both experience the same thing with the same build.
Ah, you play in 3d! Yes, my friend with the 480's also plays in 3d @ 1920x1080 for Skyrim and everything else he can these days. We've noticed that 3d only has about a 20% or so GPU/CPU overhead, but it can push you out of the 60fps zone easily as of course we need 120fps for a perceived 60fps now...that's too much for a pair of 480's. Plus, really, some more CPU grunt over his 2600k @ 4.8 would be useful too, Skyrim does use more CPU than you'd expect.
I do get the whole hassle factor thing. My loop was working perfectly, however the (external) rad had a manufacturing fault so had to be returned - major hassle. Then, after fitting the replacement rad, one of my EK Compression fittings failed (I'll never buy another EK compression fitting) killing my upper GTX 570. Major hassle once again. While I, like yourself no doubt, do enjoy building a rig, I do want to get some play time too! One of the reasons I did an external assembly is that I can easily transfer it to another build...it takes 2 minutes to unplumb it, if that. Draining is easier too, as I'm just draining the coolant in the case, so what's contained in the pipes and blocks - takes a couple of minutes.
Thermal pads - I just dug out the boxes to check this...
My old GTX 570 rev 1.0 block - so same PCB as a 580 - had THREE thicknesses of pads, a 0.5mm, a 1.5mm and a 2mm. The last one was for one component only.
My newer GTX 570 rev 2 (the SE 1.1 block) for the new, shorter "HD" GTX 570 had TWO thicknesses of thermal pad, a 0.5mm and a 1mm.
I still have the remaining off-cuts of pad, so I can see the difference between them quite readily. I wonder if your blocks only came with the ONE thickness? That would be really bad as, if too thin, you'd not get the contact - hot hot hot, and if too thick, well, the extra clearance that would potentially give you on some components, would mean zero contact on others. That could be the source of all your troubles!
Scoob.