My 2 cents:

Seeing as you were the chip leader and with the blinds being 600 I think your raise was way too small. 99 is a decent hand but not a great hand. I would raise big to let everyone know that I think I have the best hand and that they are going to have to pay to see the flop with me. I'm talking at least 2000 raise if the blinds are 600. Even 2000 is low....maybe 2500-3200. I am perfectly happy stealing the blinds with 99 because yes it is a good hand but it is so easily beaten if you are called because you just know any callers are going to have overcards most of the time.

Bottom line is that if you had raised bigger any sane person with a low pocket pair would have folded because small pocket pairs are worthless without help and if the cost of seeing the flop is too high then its an easy laydown. Now if you raised the nines big and you had a caller or a reraise then thats a signal that you could be in trouble. In that case I would either fold to a big reraise or if he just calls then play very cautiously after the flop maybe putting out a decent sized test bet and planning to fold if he calls or reraises.