I had a therapist tell me one time I was giving "negative vibes" to men.....And I wasn't aware of that. You might consider seeing a professional to get some feedback. They are trained in noticing all sorts of things about people. I really can't tell what might be happening with you from your just telling me about it, alas.
You did say sometimes your facial expressions might not look friendly. We only have so much control over things like that, especially if we are busy talking..... You also said you are a bit shy, at least at first.
Speaking of first, are you ever asking people first about being on FB or do you wait for them to ask you?