Strange Performance Issue / R290X

I am facing a weird problem with the R290X performance on a newer Intel chipset. I hope I just did something wrong and I will quickly be pointed in the right direction

I have used two test systems and two Radeon GPUs:
System #1
Motherboard: X8DTG-D (Supermicro)
Chipset: Intel 5520 (Tylersburg)
CPU: 2x Xeon E5645 @ 2.40 Ghz
RAM: 32 Gb @ 1333 Mhz
Slot: PCI-E 2.0 x13 [GEN2]

System #2
Motherboard: X9SRG-F (Supermicro)
Chipset: Intel C602 (Patsburg)
CPU: 1x Xeon E5-2630v2 @ 2.60 GHz
RAM: 32 Gb @ 1600 MHz
Slot: PCI-E 3.0 x16 [GEN3]

The Radeon GPUs are a 6990 and a R290X. Both have been used before with heavy loads and the hardware is perfectly ok. Hardware switch in the correct position, tuned with OD6, identical software on both machines.

O/S: Linux, Kernels tried: 3.2.0-4-amd64, 3.12-0-amd64
AMD Driver: fglrx 13.25.5 [Dec 6 2013]

I see the following performance measurements (oclHashcat -b -m1000):
On the System #1
6990 - 20048.4 MH/s
R290 - 17480.4 MH/s
On the System #2
6990 - 20123.4 MH/s
R290 - 14764.8 MH/s

I was quite surprised by the significantly lower performance of the R290X on the second system. The only differences I can spot is that on the System #2, the R290X is detected as PCI GEN3 - supposed to run faster if anything, and the BIOS is UEFI.

Any ideas?

Cheers,
ecos