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The only time I did have issues was early on with NVidia drivers still on the system...once I took NVidia drivers off, some (but not all) 3D apps didn't work anymore / work right with the AMD 7990s...a complete reinstall of AMD CCC after cleaning out everything else solved those.
I have been running two 7990 Maltas initially for work and now for fun for a few months, and just water-cooled them. What you describe sounds more like driver issues, and possibly memory settings. I've been running AMD 13.6Beta2 and they have been very stable so far.
The only time I did have issues was early on with NVidia drivers still on the system...once I took NVidia drivers off, some (but not all) 3D apps didn't work anymore / work right with the AMD 7990s...a complete reinstall of AMD CCC after cleaning out everything else solved those.