Florian,
I am not certain what in the OS would cause additional cores to be shown. Especially with Logical Procs disabled in the BIOS.
There is a couple things I would like to try.
Between where the power supplies connect to the motherboard is a jumper labeled NVRAM_CLR, move the jumper over with server powered off and then apply power. Once you see lights power the server back down and restore the jumper to its original location.
Then boot and see if the issue continues, if so then I would like to power down and then swap the processor in the server for another.
Thank you.