This happened in July 2008 and there were no problems. Yes, the NSEERS section should be open 24 hours, it is just that not everyone at the airport knows about it.
From what I could see, there was nothing in the departure section, so I had to go to the Arrivals area. I did see a sign for NSEERS, but that office was closed and the customs people mentioned it won't be open till later in the day. I was a little disappointed and was chatting with a security officer there explaining about special registration. He asked me to hold on for a minute and went to talk to someone. Later, he took me to a backroom where another officer asked me what I was looking for. I mentioned that I wanted to do my special registration as required by the NSEERS program. She forwarded me to an elevator in the back and asked me to go up. I ended up in the Secondary Inspection of the Arrivals area where the next lady helped me out.
My case was quite simple as I had received my GC and wanted them to make an entry in their records that I no longer needed to do special registration under my FIN. The immigration lady looked at my GC closely and said there was no need and I should be okay. I left shortly after and proceeded towards the departure lounge. If your case is simple, you should be okay.
Hope this info helped.
Stoned!