As far as I read there is no way to disable a PCI slot, so the solution is to 
force the use of the correct slot.
Check in your /var/log/Xorg.0.conf, you should find a line like this (this is 
from another computer, so the chip type will be different):

(II) Nov 24 09:47:43 NVIDIA(0): NVIDIA GPU GeForce 8400M GS (G86M) at
PCI:1:0:0 (GPU-0)

indicating that the nvidia driver found an nvidia chip at the given pci
slot. If yes, I suppose the asterisk above doesn't mean anything
relevant to our problem...

-- 
nvidia propietary driver fails to load X with geforce 310M
https://bugs.launchpad.net/bugs/643895
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which is subscribed to nvidia-graphics-drivers in ubuntu.

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