Not sure if this has already been covered ( I didn't read the next 6 pages or whatever), but this is actually a major flaw of the whole series.
Speaking from personal experience, if an enemy helicopter can detect your pos and mission (Stinger gunner instead of TOW gunner, ect), you've clearly ****ed up somewhere along the way. There's no way they would know, especially from multiple kilometers out, and if they did they'd take evasive maneuvers away from your pos rather than relying on flares to do the trick for them. The way it is now, anytime a helicopter comes within the firing range of a MANPAD, they begin popping flares like candy, even if there's no possible way for them to have recognized their position, much less identify them as MANPADS.
Beyond this, however, the Stinger in particular isn't merely an IR missile. It also has an alternative guidance system that prevents it from being jammed by flares alone. Maybe it's just because it happens to be my job, but I find it a HUGE pet peeve to see my missiles missing when I know they shouldn't be..
EDIT:
A colleague of mine mentioned that the last part was still secret. (Fairly positive my heart stopped beating there..) Luckily, it's all over the internet already;
The point is, the in-game Stingers are weak comparisons to their real life counterpart..