On a PO you place your critical (and other) requirements. Many companies include type and extent of control (we can audit you when/if we want and such) as well as things like (if it IS a requirement) ISO9001 registration required. And things like type of material, dimensions - what ever is appropriate.
You said the auditor could not tell you the difference in the two statements - s/he must be stupid to cite you when s/he couldn't rell you the difference - which is what the nonconformance was for. Really strange,
However - I will say that as I thought about this putting "QS9000 registration preferred" on the PO does not state a requirement - the word 'preferred' is the key. But then again, inclusion of the statement should not be prohibited as far as I can see. If QS9000 registration is *required*, 'preferred' will not do.