It might be that when you sit his trot, which I am going to make a guess is prett slow, more like a jog, that you are way back on your "back pockets", slumped a bit at the waste and are consequently behind the motion of the trot.
you can get away with that when sitting, but when rising, you don't want to be behind the motion of the trot or you will struggle a lot, and your leg will come out in front of you, as if you are constantly struggling up a hill. Any of this sound familiar?
Two things to consider;
Does your english saddle fit correctly? if it is too high in front, it will put you in a chair seat which creates a behind the motion position.
Does you horse have enough impulsion for you to post off of? if not, snap him a quick one with the crop and get more energy and foward movement without you doing all the work by squeezing him every step of the way.