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I'm a little unclear as to what motherboard I have in my shuttle SN45G.
It should come with a fn45 but pc-z registers it as a fn41.... the label on the board reads fn41/fn45..... any ideas ?

This seems like a no brainer.

The main difference between the 41 and the 45 is in the NB. Check the NB and look for the nvidia nForce 2 ultra label. find this and it is a 45

I assume you mean the Northbride (NB?).... it reads fn41. But that's normally the board that ships with the SN41g2 not the SN45g.

The fn41 also comes with on-board graphics , which my board hasn't.

So in summary... the board is labelled fn41/fn45.... CPU-z thinks is a fn41sp.... but the physical layout dosn't (no on-board graphics) dosn't add up.

If the wrong motherboard drivers are installed (fn41 instead of fn45), does that somtimes confuse utilities like CPU-Z ?