The matrix has very small tubes within it, the water doesn't circulate through these small tubes, rather the heat in the coolant convects along them, the "tank" at the end of the matrix where the heater pipes go in/out is just a space so the water doesn't "travel" as such through the heater pipes just the end tank.
Maybe your stat is no good or the matrix is blocked, what stat do you have, I've found wahla to be the best for me, I use a 88C, will use a 92-94 when I change it next though.
Have you checked your engine temp is up to temp, and that the flaps on the heater box are moving fully.
tabetha