As I'm back from my NYC trip I can report the following (a small trip report also...):

Arrived at STR full 2 hours before departure I found complete chaos at the checkin-counter. The security was set up without thought and so we had to wait in a very long line together with charter pax (to Greece). Their checkin was very slow and nobody waited at the KLM-counters. Finally arrived there and asked for a possible upgrade by FD-points as adivised by KLM helpdesk. The agent said that she's not possible to do that and sent me to the ticket-counter. The agent there was very friendly but said that upgrades by points could only be done at AMS and that she's expressly forbidden to handle this, even to call to AMS in advance to set me onto a waitlist. But she checked and found free seats in C - so there was hope at least...
Back again at checkin we got only 4 seats in 4 different rows for AMS-JFK as this flight would be full and she couldn't change arrangements therefore.
Arrived at AMS I found the Transfer-desks at D and E with long lines and so directly proceeded to the international Business Lounge. Four agents there, one intensly flirting with a flight-captain (and a little bit more, sitting together on one office-chair...). Asked for an upgrade by points for the four of us, my agent said without checking her computer that she's afraid that there are only three seats left (I'm not really shure if this was true or just a trick that saved her some work...). But at least we got 4 seats together - she was surprised that STR could not give us four seats as the seat assignment had several possibilities for four seats together left...
For the return flight JFK-AMS she could not help us with upgrades as she could only do that for flights originating from AMS for the same day. Only possibility for this would have been FD helpdesk 14 days prior to departure (without availability in my case...).
On the return I asked at JFK NW checkin (with a very good organised security and checkin area at terminal 4) for the upgrade by points but the agent there confirmed what I heared at AMS.

The flights were uneventful; both AMS-JFK and JFK-AMS were 90% full in Y with some open seats in C on the flight to JFK (as I could spy through the curtain). Both were about 1 hour late. Service was standard with friendly (and this time really pretty... ;-) ) cabin crew. Wait time at the terminal/gate security check at AMS was about 20 Minutes (Terminal E) and only a few minutes at JFK (Terminal 4, part A).

So another procedure that KLM could put some thoughts into: Upgrade-procedures by points at the gate - not only at AMS. It should be much more efficient to upgrade pax willing to spend their points if there are open seats before doing operational upgrades or flying with empty seats, shouldn't it?