Check the flaps on the heater box are not stuck or disconnected, also the bowden cables.
The design of the heater matrix means if it gets blocked it will still pass water no problem as it is only an open chamber at the end where the two pipes are, and it relies purely on convection for heat to travel through the matrix, so even though the water goes through ok it could still be blocked, would be worthwhile trying a flushing agent, use a Wynns one and leave in for a few hundred miles, not 10 minutes like the bottle says.
This is what I do, and the crap that comes out and accumulates in the expansion bottle is unbeleivable, and will of course take you an hour to degunge afterwards but worth it.
tabetha