You aren't doing anything wrong. In fact, the inability to orgasm quickly is beyond your conscious control. It sounds like you are experiencing an unconscious defense called 'inhibition.'
Inhibition is an involuntary holding back that is designed to protect or defend the self. Why would you need protection?
You mentioned that you don't see your partner as often as you would like. I have the idea that you may be unconsciously 'sitting on' or cutting off from your desire for her in order to not feel so frustrated during her absence.
If this cut-off is occurring, then it would also make sense that you would have a hard time turning yourself back on again when you resume contact. This could explain why you find it hard to fully respond on a sexual level when you are finally together.
If this is so, just becoming conscious of the defense is the first step. You can then consciously choose to stay fully in touch with your feelings, including your feelings of frustration, even when she's far away. Doing so will enable you to be more in touch and responsive when you are together.
Good luck. Long distance relationships are trying.