I have a 2003 a4 1.8T 5 speed. Timing belt, water pump, thermostat have all been replaced. Heater core is fine, radiator is fine. The problem is, heat will blow out, then after a while it stops and comes out cold. After 10 or 20 minutes, the heat kicks back on and no one seems to know why. Has anyone encountered this problem?

 

how do you know the heater core is fine....? because if it was, You would have heat.

If the timing belt / water pump was replaced recently, it sounds like air in the system

 

Ummm, not to second guess you but there is a TSB for this exact issue at audi for that engine. Its a coolant plug under the intake manifold that causes this exact issue, it gets air in the system and plays havoc with the heater. Take it back to the dealer, or at least a dealer that aren't idiots.