Well.... does the bios see/says all 6 cores and HT is turned on? if not, that might help.
If so then have you reinstalled Ubuntu to see if that solves it?
If neither solve it then i would recommend heading over to the linux section of the forums where this question maybe more easily answered by the more experienced linux users. i've touch the latest ubuntu although i've only used it on dual core cpu's. It just sounds like to me though like an OS limitation/restriction to me than a hardware issue. Maybe you'll need to run the sever version of it? I dont know but im sure if anyone can figure out, it's them.
Although what kind of cpu processing you doing? Just out of curiosity as i could see something like your setup for distributed computing projects (like Folding@home or BIONC) or an intense mathematical calculation program.
Why does the latest Ubuntu only recognize 8 cores on my Core i7 980x? Windows 7 is able to recognize all 12.
Intel Core i7 980x
2 x 2 GB dual channel DDR3 1600 G.Skill Ripjaws
350 GB Western Digital Black Notebook form
Don't laugh at the unbalanced system - it's used purely for CPU processing.
Have you compiled a custom kernel or are you using the stock kernel shipped with Ubuntu? I don't use Ubuntu, but when configuring the new kernel in the SMP section you can select how many CPU's you have. Alot of older based distributions set this to an arbitrary 8. The linux kernel (and windows for that matter) see each HT core as its own individual processor. Yes, your CPU physically has 6 cores, but with HT on, the hardware tells the OS that there are 12. There are plenty of documents on the net giving detailed instructions on how to make and install a custom kernel, google it. This is where the linux boys are seperated from the men.