Hi irishguy28, thanks for the reply.
As I said in my first message the issue is not with the booking class, it is that the system somehow identifies the miles as already credited although they are not.
To answer your question, the ticket was on V fare, which is supposed to award around 3000 miles for NRT - ZRH (LX161) and 400 miles for ZRH - MAD (LX2032), so around 3400 miles in total. Both flights were operated by Swiss, no code share.
What is interesting is that for my inbound flight into NRT (again with Swiss) the miles were awarded very fast and automatically, without any need for manual claim. The issue arose with the outbound flight for some reason.