The saga continues!
I had exactly the same problem yesterday, AMS-CPH : the e.check-in machine issued a boarding card without the e-ticket number. By now I knew better than to present this boarding card at the gate, so I asked the agent at the Schengen RW lounge to look into the matter. She was very friendly and helpful, and came over to me a few minutes later with a new boarding card. She gave as her opinion that the error must lie with my travel agent, as "the system" did not identify my reservation as an e-ticket. That of course begs the question how my travel agent can issue me with a detailed KLM confirmation that starts with the words electronic ticket. . . .
Next time I'm in the Netherlands I shall have to sort this problem out once and for all.
johan