or you started out with gunky looking coolant and the heater core is plugged enough with the gunk that even with what looks like good flow*, it wont work.. or you might have both problems.
*If you think just a couple passages open wont look like good flow, pull off your shower head or the aerator on your sink faucet.
- Bad water pump will result in the source hose to heater being hot, exit hose from heater to WP being cold.