My guess is that when you didn't check in 30 minutes before departure they gave your seats away to standby passengers (or last minute purchasers). By the time you finally moseyed on up to the counter, there were simply no seats to give you. Since the plane was full and if everyone was on board and accounted for, then they could leave as early as they want. Maybe some bad weather was rolling in and they wanted to beat it? Also the time printed on your ticket is not guaranteed. Planes can sometimes leave early and many times leave late which is another big reason to get there extra early.
I just got back from a Florida/Bahamas vacation yesterday. Last week we arrived at our tornado damaged St. Louis airport 90 minutes early, and had no issues checking our bags (I *LOVE* Southwest and their free bag checking.. so nice not to keep a carry-on with you everywhere), getting through security, getting a quick snack and hanging out at the gate for a bit before having to board. Then again, St. Louis is one of the better airports to deal with.
As for Fort Lauderdale, by the time we turned in our rental car and got to the terminal yesterday it was only 60 minutes early and they seemed really busy. I was a bit worried but then I noticed that the flight had been pushed back (delayed) for 20 minutes so then we were all good. Actually sailed through TSA both times without a hitch, even after forgetting to take off my watch and setting off the metal detector!
Security on the ship was much more lax, although I did get felt up by a Bahamian Security agent but he was all cool about it, even (jokingly) telling my GF not to be jealous about the physical contact!

Coming back I thought it was funny that Customs let me sail right through while a middle-eastern looking family of nine (with four small children and three young teens) was being whisked away to their examination room, although their ignorance of the English language might have had something to do with that.
While I'm on the subject, I though it was funny that while taxiing for takeoff in FL a small child was just SCREAMING his face off. I thought it was an infant until I head "I don't like airplanes, I don't like airplanes" and he jumped up. The kid must have been about four years old. Anyway, thankfully shortly after takeoff he finally quieted down and it ended up being a pleasant flight. After getting off the plane and going towards the baggage claim, I heard a man say "Say bye-bye to the airplanes!" and I looked back to see that same exact kid start screaming once again and crying "I don't wanna leave! I don't wanna leave!"

Kids crack me up!! (although my GF wasn't pleased)