One of my reference letters did not show up as "submitted" until around 8:15 last night and I got really anxious that I would be disqualified. I thought I would post what I found out from NSF, just in case anyone else is in the same boat.
I emailed the program office (info@nsfgrfp.org) to ask about the status of my application. After explaining the situation, I received the following reply:
"The FastLane reference letter module switched off at 8:00 p.m. yesterday, so references were not able to log in to submit references after the deadline. We understand that the FastLane module simply would not allow references to submit after the deadline, so if the letter shows up in the FastLane status page as submitted, then it is considered officially submitted. (It may be the case that, due to a high volume of traffic, a reference may have been logged in and pressed the "submit" button before the deadline, but the submission process may have completed a few minutes late. As long as they were logged in and pressed the "submit" button by 8:00 p.m., the deadline would be considered to have been met."
To summarize, if your letters show up as "Submitted" on the manage references page then you are in the clear.