Water source might be the key thing here. If it's a stream that flows off the map edge, it's probably taking the stream outlet rather than your aqueduct. That is, the pipes fill as long as water drops gravitationally into the hole. However at some point the physics engine stops pathing for falling water. (No doubt there is some form of short circuit built in to save checking every path for every piece of water when most of it will not actually have open space to fall into.) The only pressure trigger remaining is from the stream inflow and it will tend to prefer lateral movement along the watercourse over any "upwards," even when there is open space several z-levels down.
If this is the case your aqueduct is engineered perfectly, it's nature that is incorrect! A common complaint of dwarves.
For one possible solution, you could try some scheme to dam the stream at the downstream map edge, so that the water builds up to 7/7 there and the upstream flow checks more spaces. Only a partial dam is necessary, such that the map edge outflow is less then potential inflow.
Caution: this can and will cause water to rise all the way to the starting level, unlike my previous pure gravity diagram.Or you can try to restart the vertical falling as PatrikLundell suggests. I guess that's not working for you, at least not whatever plan you tried.