I've also found the Javelin drastically less accurate this patch (2.03), earlier I played Guarding the Far Flank by PBEM, with my opponent and I swapping sides after the first match and we both found the Javelin to have an atrocious hit rate. (6 misses over 2 turns, which was all the ATGMs fired)
Specifically, it seems that the missile fails to drop attack and instead just sails over the target and off the map.