Why does my baby wake at 3:30am?

My son is 9 months old now and has never been the worlds most 'Elite' sleeper. Lets put it this way ... i don't think I've slept more than 3 hours in one block since he was conceived lol.
Over the past 5 months or so, I have managed to battle his bed time protest down from up to four hours to about half an hour which is a great relief but he is still waking in the night. He has two naps during the day and goes to bed at 7:00pm (usually asleep by 7.30). He wakes around 12.30 but resettles without too much protest. He then wakes at approx 3.30 and although he wants to be asleep something is bothering him. He just wriggles and wriggles and wriggles till about 6am. I've tried putting more/less clothes on him .. makes no difference .... have tried breastfeeding him ... which helps with the wriggling but doesn't send him back to sleep. I tried cuddling him, let him cry for a while, giving him a bottle of water, rubbing his feet and belly. I guess it could be teething but he's been showing signs of teething since 2 and half months with no results yet. Any ideas as to what might be bothering him? and anything I could try to help?