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The problem is inherent to dual-GPU setups, from both manufacturers.
Stutter is common across both vendors for sure, but AMD's stuttering issues are incredibly more pronounced when running triple head. The difference between 60 frames on a single monitor and 60 frames in Eyefinity is very large. Single monitor is smooth as silk, you might see the occasional bit of stutter but it always springs back to a fluid feeling. Triple head on the other hand never looks fluid like a single screen.
The HD5s did perform quite badly both in eyefinity and in crossfire, so that certainly isn't going to help. Before you write off the technology I'd say try and use an HD6-based system and then report back. Things are much improved.
This. 2x 6950's in Eyefinity works amazingly well. Smooth.