Hi Nicolas, it doesn't sound like you've missed anything here and it's likely to be down to how the software works. Despite you being able to nominate a default nominal account, with cost centre and department, for your landed costs under Stock Control Settings, only the account number element of that gets used when recording the invoice.
At that point, it will try to use the default cost centre and department from the supplier record the invoice is being posted to. If that combination of nominal code, cost centre and department doesn't exist as an account on the nominal list, you will see the 'Intended For //' narrative on the resulting invoice when posted.  

This is something you have control over on the stock element of the Purchase Order where, in your Purchase Order Processing Settings, you have the option to choose whether you use the cost centre and department from the stock account or the supplier account, so it would be worth raising this through our Ideas Hub to have that same control over the Landed Costs side of things.

Many thanks.