I think I would...

2-4 people see the flop. I flop top 2 pairs or a set (the board isn't paired). There are 2 of the same suit on the board, and I don't have any of them.

Confident I have top hand at that moment, I've been pushing in.

But anyone with 4 to a flush is close enough to 50% at that point to call.

The odds say that the combination of someone having to be 2 to a flush at that point plus the under 50% likelihood that they'll make their flush gives me somewhat better than even odds to do what I'm doing.

But the reality is that somewhere around 45% of the time, I'm out of the tourney or crippled when I do this (assuming I'm not way ahead on chips).

I think maybe my move is a fishy one here... I should wait for a better advantage to put my tournament on the line.

Thoughts?

I wouldn't call this a leak. Here is an example to illustrate why I think you are wrong to look at it this way.

If you make top set on a board with 2 suited cards, you are more than a 70% favourite to win at the river. Your opponent only has a 30% or less chance of winning- don't forget that even when he makes his flush, if the board pairs, you still win with your boat. So I think your odds are a little off- he is much worse than a 50/50. Obviosuly these odds change when you get to middle or bottom set, or two pair, but I am sure you see my point.

The important thing in this spot is to make sure your opponents are not getting the right odds to call. Betting the pot, therefore, or overbetting it, as you advocate, will certainly do this. In fact, you must bet the pot to protect your set. Of course this will not stop the fish calling you, but they will be mathematically wrong to do so, so, in the long term, this will make you money.

This is all dependent on stack size, how many left etc, as everything else is especailly in an SnG. But I firmly believe that not betting out with a made set on the flop, even if it is bottom set, is a big mistake, and one that will lead to you playing scared. After all, if you ain't going to push it here, when are you going to?

What I would do in that situation -- VERY confident that I have the best made hand --

On the flop I will bet, but NOT all in. I will bet the smaller of the following two amounts:
(1) The pot size
(2) The amount that will make the pot on the turn equal to my remaining stack size on the turn IF I am called by exactly one player.

If the turn is not a flush card, I will then go all in.

Firing a big bullet on the turn really puts the pressure on the flush chaser. It is a VERY poor move for him to call you most of the time, and even if he does call you, you have a solid 75-80% chance to survive and double up!

Hope that helps.