I've found a solution to my problem : it was ACPI-related.
Some ACPI options where disabled in the BIOS (due to problems with previous 
versions of ubuntu), I enabled them and the second core is now recognized.

Now, I'm wondering how ACPI options can interfere with SMP capabilties
of the motherboard and why both cores where recognized on 9.04 even with
these options disabled (something must have changed in ubuntu
motherboard recognition I guess) but at least it works properly now.

Of course I'm still available if more info is needed on this issue.

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Athlon X2 not recognized as dual core
https://bugs.launchpad.net/bugs/437821
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