Hi, heater fan is blowing cold air and sometimes warm air depending on when i start the engine.

Low coolant, if there is an air pocket in the engine it will make it to the heater core. Once there , the air coming out is cold/cool. Once the coolant fills the heater core, it gets hot. If the coolant is fine hot or cold, then have the HVAC system scanned.

To troubleshoot this types of problem,click the link below :----http://howtobyme.blogspot.in/2012/02/heater-blows-only-from-defrost.html
--------Go through the procedure to confirm the issue.

------
Engine Overheats and heater blowing cold?

http://howtobyme.blogspot.com/2011/11/engine-overheats-and-heater-blowing.html

---------
Heat blows cold on drivers side and hot on passenger side?

http://schematicsdiagram.blogspot.com/2011/12/heat-blows-cold-on-drivers-side-and-hot.html

-----------

No heat on car? http://technoanswers.blogspot.in/2012/02/no-heat-on-oldsmobile-silhouette.html

------------
Heater blows intermittently and temp gauge goes erratic? http://technoanswers.blogspot.com/2012/01/heater-blows-intermittently-and-temp.html------------Heater blows cold? http://schematicsdiagram.blogspot.in/2012/02/heater-blows-cold.html
---------Car heater blowing warm, but not hot air? http://schematicsdiagram.blogspot.com/2011/12/car-heater-blowing-warm-but-not-hot-air.html-------- Heater/AC blower motor not working?

http://technoanswers.blogspot.in/2012/02/heaterac-blower-motor-not-working-on.html

------------
A/C, heater, defroster fan, not working? http://technoanswers.blogspot.in/2012/02/ac-heater-defroster-fan-not-working.html Heater problem? http://technoanswers.blogspot.in/2012/02/heater-problem-on-isuzu-trooper.html---------

This will help.Thanks.

For this types of problem,i suggest you to check this help links:----Car heater blowing warm, but not hot air?http://schematicsdiagram.blogspot.com/2011/12/car-heater-blowing-warm-but-not-hot-air.html
---------A/C, heater, defroster fan, not working?http://technoanswers.blogspot.in/2012/02/ac-heater-defroster-fan-not-working.html
--------Heater problem?http://technoanswers.blogspot.in/2012/02/heater-problem-on-isuzu-trooper.html
---------Engine Overheats and heater blowing cold?http://howtobyme.blogspot.com/2011/11/engine-overheats-and-heater-blowing.html
-----------Heat blows cold on drivers side and hot on passenger side?http://schematicsdiagram.blogspot.com/2011/12/heat-blows-cold-on-drivers-side-and-hot.html----------------This will help.Thanks.

low fluid level or heater control valve may need replace..check hoses going to heater core...if cold...between heater control valve and heater core..replace control valve

check your anti-freeze level, I'd bet that you're a little bit low!

First you have to identify what causes the problem.
To do this you have to:
1) When engine is cold check the level of coolant. If it is low fill it up.
2) Start engine and check if engine reaches regular temperature. If your engine is not heated enough it means your thermostat does not work properly and should be replaced.
3) If engine temperature is normal, then check the temperature of pipes that go to/from heater core. These pipes are located up the fire wall (easier access is from the passenger side). If pipe/pipes are cold (even engine is worm) it means you heater core is plugged and should be flushed. Keep in mind, flushing the whole cooling system is different from flushing heater core.
4) If pipe/pipes are hot/warm, turn off the fan, switch controller to the hot position, wait for 3-4 minutes and turn on the fan. Note if the cold air blows first or warm air blows first but it cools down in 5-10 seconds. If the air blows cold than it is most probably the problem with blend door or blend door actuator.
5) If air blows warm first and then cools down, then while running engine and remaining the transmission in PARKING position, press on the gas pedal until your engine reaches 3,000 RPM. Check if your heater blows warm/hot air. If it does, then your water pump does not work properly and should be replaced. If the air still cold, I would suggest to flush the heater core.

It is most probably the problem with blend door or blend door actuator. But just in case I would suggest to follow the entire procedure:

First you have to identify what causes the problem.
To do this you have to:
1) When engine is cold check the level of coolant. If it is low fill it up.
2) Start engine and check if engine reaches regular temperature. If your engine is not heated enough it means your thermostat does not work properly and should be replaced
3) If engine temperature is normal, then check the temperature of pipes that go to/from heater core. These pipes are located up the fire wall (easier access is from the passenger side). If pipe/pipes are cold (even engine is warm) it means you heater core is plugged and should be flushed. Keep in mind, flushing the whole cooling system is different from flushing heater core.
4) If pipe/pipes are hot/warm, turn off the fan, switch controller to the hot position, wait for 3-4 minutes and turn on the fan. Note if the cold air blows first or warm air blows first but it cools down in 5-10 seconds. If the air blows cold than it is most probably the problem with blend door or blend door actuator.
5) If air blows warm first and then cools down, then while running engine and remaining the transmission in PARKING position, press on the gas pedal until your engine reaches 3,000 RPM. Check if your heater blows warm/hot air. If it does, then your water pump does not work properly and should be replaced. If the air still cold, I would suggest flushing the heater core.

First you have to identify what causes the problem.
To do this you have to:
1) When engine is cold check the level of coolant. If it is low fill it up.
2) Start engine and check if engine reaches regular temperature. If your engine is not heated enough it means your thermostat does not work properly and should be replaced.
3) If engine temperature is normal, then check the temperature of pipes that go to/from heater core. These pipes are located up the fire wall (easier access is from the passenger side). If pipe/pipes are cold (even engine is warm) it means you heater core is plugged and should be flushed. Keep in mind, flushing the whole cooling system is different from flushing heater core.
4) If pipe/pipes are hot/warm, turn off the fan, switch controller to the hot position, wait for 3-4 minutes and turn on the fan. Note if the cold air blows first or warm air blows first but it cools down in 5-10 seconds. If the air blows cold than it is most probably the problem with blend door or blend door actuator.
5) If air blows warm first and then cools down, then while running engine and remaining the transmission in PARKING position, press on the gas pedal until your engine reaches 3,000 RPM. Check if your heater blows warm/hot air. If it does, then your water pump does not work properly and should be replaced. If the air still cold, I would suggest flushing the heater core.

the most probabale cause of this would be a disfunctional hear core if you replace your heater your heater will more than likley work the the way it's supposed to

With the car warmed up,feel the heater hoses,are they both warm/hot near the firewall in the engine compartment?If they are both warm/hot,then the heater core should have circulation through it and it may be a "blend door" issue in the heater a/c assembly.If they are not warm/hot then the heater core could be dirty and plugged up and needs to be flushed.
If the above does not help,a drain and vacuum of the cooling system and vacuum refill will remove any trapped air.
Sometimes,clamping off the top rad hose and holding the engine rpm at 2000 rpm will force trapped air out of the heater core.(Watch temp gauge when trying this)
Lastly,a NEW thermostat doesn't mean its working correctly.