In the most recent edition of White Wolf's World of Darkness role-playing system, there is a Flaw called "Behavior Blind". A character with Behavior Blind has great difficulty picking up on the subtleties of social interaction, which can place one at a severe disadvantage in, say, the Vampire: the Requiem game in this system (in which, among other things, centuries-old vampires while away their unlives playing politics). One of the effects of Behavior Blind is that while the character can still have the skill of Empathy, he/she will be at -3 on all such rolls (that is, any attempt at using Empathy to persuade someone of something, or guess at their motivations, would require three more successful rolls against the Empathy skill than a normal character).
Sounds kind of like what we're talking about here - the Empathy is there, we just aren't getting enough successes on our rolls...
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