Flares are 100% working, as you said, you just need to time it right. Don't use them until the locked sound becomes hideous. There's 3 stages to the sounds.
The first beeping noise is saying that someone is tracking and locking on to you.
The second stage noise is that they have acquired a lock (this is where you should try and evade, turn hard etc to get out of their target reticule).
The third stage is where you deploy flares. This is a nasty sound that basically means rockets are locked on to you and smashing through the air as quick as they can to get to you. Deploy the flares here. I usually wait a second or so before deploying them because most pilots will fire off both heatseakers - which has a slight delay between shots, so I try to make sure that both rockets are in the air before I dump flares! Otherwise they could just save the second rocket until you're pass the flare range.
There you go, Jet Survivability Training 101
*EDIT*
From this, you should learn how to counter the above quite quickly. Try not to fire both missiles at the same time if you know they haven't dumped flares. If they have dumped flares, hit them with both rockets.
Also a tip, as you launch the missiles, swap to the chain gun and get a few hits with that. The reason being is that both rockets will NOT destroy a jet, only disable it and send it hurtling around in the sky. Most people will jump out, meaning you get no kill. If you can land a few good main gun shots on it before or as the rockets are hitting it, you'll get the disable, kill and destroy bonuses at the same time, instead of missing out on the kill and destroy.
I will definitely keep this in mind.
