BTw, have been playing with the mining rigs I have here - I have a machine running windows 8 with 2 x 280x and I get 750 from each, then plugged in the BAMT with 13.12 AMD driver and restarted on that same machine, and only got about 550 with each card, on exactly the same settings...so it's definately an operating system/driver problem..nothing to do with hardware in my case. However, on windows you can use the AMD catalyst center to activate the overclocking, just wondering how that is done via Linux - aticonfig?..
In linux you just tell the GPU what to do, and the drivers do the rest. IE, if you want the clock rate to be 1200 or 1400, you simply tell it. No need to run anything else. In windows, you have to use catalyst. However, linux can't undervolt via software, whereas in windows it can. For linux to undervolt, I have to flash the GPU bios with the undervolt setting.
For example if I want to OC my cards and tell them to go from 1130mhz to say, 1800mhz, I simply tell cgminer to flip to 1800mhz.
Usually when there's situations like this (whether it's mining or playing games), it comes down to driver issues based on hardware setups. For instance, most hardware has more driver support on the Windows side by default, due to it having more market share. GPU driver support is even more heavily geared toward the Windows users because most gamers are using Windows.
So it's likely a driver/hardware thing, but Windows has more access to more up to date drivers. I get better hash results in linux/debian (bamt) than I do with windows, probably because my hardware (ASRock 970-EX4 w/ everything disabled but USB and GPU) is 100% what BAMT was built for, so all the built-in drivers are prepped for the hardware.
Using other hardware, it'll be mixed. And when building linux from the ground up, unless you're good at building the drivers (sometimes having to use an old driver, which might take days to figure out) from scratch, it could lead to pulling your hair out.
That's another thing--I disable literally everything on the motherboard (via BIOS), except for the USB ports and built-in ethernet port. This prevents anything unused from taking power, and prevents any "unnecessary" driver issues. SSD is disabled, IDE, Floppy, Serial ports, IR ports, the whole 9 yards.. it's all disabled.
Glad to hear you've got some more hash rates!