I don't have any difficulty with social cues or understanding innate human interaction. I am popular in the workplace because I'm forced to interact with others. Almost all my friends are from work. By contrast, none of my neighbors know me and probably think I'm odd because they never see me. That's because, when I have a choice, I will always pick avoiding social interaction due to fear. Whenever I leave, I check the peephole to make sure no one is around. I have gone a week or more without leaving my home. If not for needing food and to go to work, I could probably go months without leaving. And this is driven by fear of human interaction.
I can appear completely normal in social interactions. I understand eye contact and not to linger too long. I understand the need to balance talk and listening when having a conversation. I get jokes and subtle humor. Fist pumps get me excited. No one had to teach me these things. And most of my co-workers think I'm completely normal in social settings, though on the quiet side. But when given a choice I withdraw due to fear. In High School, I spent every single lunch hiding in the library or a bathroom stall. I did not know what the cafeteria looked like. I didn't go to a single party or a single date due to crippling fear. But this fear was not the result of feeling confused over social cues or behavior.
The other thing I'm really interested in is a deep examination of your comment "When I have a choice...due to fear." Is it always due to fear, or due to preference? That could be a breakthrough for you, to examine this...there's a difference between the two, and a lot of times I would ascribe that feeling to fear, it was actually preference...a choice to avoid the fear. If I could push through that--rarely by my own will, but more often just by circumstances--the fear would subside and I would realize that the preference was what was broken. Not that it is fixed now, or anything...
Rather, it's like a pervasive pessimism. A more-cerebral problem, where you tell yourself that social interaction requires a safe reason (classes, work) and avoidance due to fear of some future hypothetical failure.