I have the exact same issue with all of my rigs, but have found that it is only with Windows.
As an example here are my rigs with 7970s. Each has Windows 7, afterbuner 3.00x beta 10, catalyst 13.3, + the following:
Rig 1. 2x7970 - ASRock OC Formula, 2500k, 8GB Ram, SSDs, + 1000 watt PSU
Rig 2. 3x7970 - ASRock 970 Extreme4, Sempron, 4GB Ram, SSD, + 1200 watt PSU
Rig 3. 2x7970 - ASRock 970 Extreme4, Sempron, 4GB Ram, SSD, +1100 watt PSU
These rigs have unfortunately had 7970s shuffled between them too many times due to hardware related issues.
Rig 1. For comparison (2x Visiontek)
1090mv / 1080e / 170m = 649.x Mh/s per GPU
Rig 2. With 4x7970 (2x Visiontek, 1x Powercolor, 1x Sapphire)
1169mv / 1110e / 170m = 645.x Mh/s per GPU (Visiontek)
1094mv / 1050e / 170m = 611.x Mh/s per GPU (Visiontek)
1056mv / 980e / 170m = 568.x Mh/s per GPU (Powercolor)
1169mv / 1110e / 170m = 645.x Mh/s per GPU (Sapphire)
Rig 2. With 3x7970 (2x Visiontek + 1x Sapphire)
1169mv / 1110e / 170m = 659.x Mh/s per GPU (Visiontek)
1094mv / 1050e / 170m = 623.x Mh/s per GPU (Visiontek)
1169mv / 1110e / 170m = 659.x Mh/s per GPU (Sapphire)
Rig 2. With 3x7970 (2x Visiontek + 1x Powercolor)
1169mv / 1110e / 170m = 652.x Mh/s per GPU (Sapphire)
1094mv / 1050e / 170m = 619.x Mh/s per GPU (Visiontek)
1056mv / 980e / 170m = 585.x Mh/s per GPU (Powercolor)
Rig 3. With 2x7970 (1x Visiontek + 1x Sapphire)
1094mv / 1050e / 170m = 621.x Mh/s per GPU (Visiontek)
1169mv / 1110e / 170m = 656.x Mh/s per GPU (Sapphire)
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The weird thing about it is that it follows no pattern. The same Sapphire 7970 with two other 7970s in that system running generates 14 Mh/s more than if I add the Powercolor card into the system. But, if I put it in a system with only one other card running it generates -3Mh/s. It is something whacky with Windows and 7 series GPUs.
The first rigs I ever put together were 4x5870 rigs with xubuntu 11.04. Each GPU ran at 980e / 170m and generated 433 Mh/s. I recently had to split some of my rigs due to not having enough risers. Using the same 11.04 cd, catalyst 11.6, and SDK 2.5, two 5870 at the exact same settings till got 433 Mh/s. If that were Windows they'd somehow magically be getting 450 ish Mh/s.
I'd use linux for all of my rigs, but I need to have the ability to undervolt my 7970s to keep them cool as I live in a nuclear inferno. The only thing I can think of is that it has to have something to do with either MSI Afterburner, bios, or Windows power saving feature. At this point I've tried powered risers, moving power supplies aroun, testing voltage input from the wall, different catalyst versions, etc... I wish someone could figure this out as it is extremely annoying.
power saving mode? didnt even consider that