I don't think chaff rejection is the problem. After observing aerial battles between AI i've noticed the only radar guided missiles that score a hit is the R-40 and the AIM-54C. Mainly because they have the thrust to keep going. Every other radar missile loses energy half way through their flight path and just sail to the ground. They definitely try to guide to a head on intercept with aircraft but they just don't have enough energy. Even when falling they don't pick up speed, or keep it, they just steadily lose it.
Most of the aircraft involved in the fight are at excellent skill level.
To add on to that, I've noticed a lot of IR-guided missiles exhibiting odd behavior - if they've gone ballistic, they'll just float to the ground at decelerating speeds, also a problem with the radar guided missiles.