So I got some debugging on a 6990 and found that, of course, it does things differently to the 5970.
I've committed some changes to the git tree which should detect 5970s and 6990s reliably on linux, and mumble mumble something maybe on windows. I have at least one report of success on windows with 5970 already.
Give it a go and report back!
I gave that windows build a spin and unfortunatly it doesn't work like it should.
I have 2x6990, so 4 GPU's visible for cgminer. I've ran it with 3 gpu's enabled, one disabled. By looking at the temperature, it is clear that cgminer is not showing the correct temperature for the correct core. Also, this version does not show temperatures for cores that are disabled, I think it would be useful if we still can see that.
Next remark: I see (always have, unchanged in this version) for my 2 first cores the RPM's for the fans, but the other 2 just show a percentage...
This is a windows machine, yes? Was this one where the two GPUs from the same card would be not one after the other? I don't know if I can pick those up at all. As I've said before, false positives for linked GPUs would be a big problem whereas false negatives would be no worse than current releases of cgminer. I'll try and make a debugging version for windows which might give me more information.