You've found that there is a highly subtle bond between the two of you that just can't be defined. You feel attracted to one another on a deeply emotional level, and you probably felt it from the very beginning; but at the same time, you both sense that things just aren't quite on track between you. Something deep and important is missing, and if you haven't been able to pinpoint it -- no easy task -- it'll continue to bother both of you, but especially your partner.
This subtle problem is related in part to the fact that you two communicate both verbally and non verbally, and the nonverbal communication between you is tense. It's as if you're each sending out mixed signals. You have a tendency to transmit a very real feeling of annoyance or frustration that causes your lover to react by pulling away, and in turn, you feel the distance...and so it will proceed. Then, when you're sharing a moment of warmth and intimacy, your lover will be wondering, Is this person being completely honest with me? Can I really trust their feelings for me? You need to work on making them believe the truth of your feelings. It might actually be the case that your feelings for each other fluctuate frequently. The best way to deal with this is to speak honestly in each moment be as clear as possible with each other.