You're definitely on the right track. Human communication is rarely just about the words that you speak. Your speech intonation, pauses, body language etc. speak volumes. Those that don't understand these things well tend to not "get" what others are trying to tell them via all the non-verbal stuff.

Initially it seemed extremely confusing to me; why would someone ask/tell me something when they meant something different? What did they really mean when they said something? Those questions continue to cause me much anxiety but I am beginning to learn more about these non-verbal communication skills.

It kinda make sense that this is more common with nerds/geeks: we spend an awful lot more time with ourselves and things we like doing rather than socially with peers/friends/relationships. The people who tend to be more social, learn more social skills this way... kind of a chicken and egg problem.