I'm running Ubuntu 10.10, Catalyst 11.3, and ATI Stream 2.3 (I've also tried 2.4, 2.1 and 2.2 aren't supported for my card).
With both poclbm and DiabloMiner I'm unable to access the second core of my first card. With poclbm I can use -D 0 or -D 1 and in both cases it uses the first core only. I confirm this using aticonfig to check the current clock speeds and temperatures of each core. When I put a second 6990 into the same system I am able to use both cores of the second card without problems.
I'd like to stick with Linux. Is it possible to not start X in Ubuntu, and if so, would that help?