1999 chevy malibu leaking coolant. not the water pump not the intake manifold. Not the hoses or from the resevoir. Could it be from the freeze plugs? if so where are they or it located at on a 1999 v6 chevy malibu??

On the block ( the bottom part of the motor ) below the intake manifold

I had a 2000 malibu 3.1 and the manifold gasket was leaking. Model years affected, 97-04. Check the recovery coolant tank and if it looks like a milk shake instead of coolant, then you have a bad intake manifold gasket. I replaced mine a few years ago and all was fine. Engines affected are the 2.4-3.1-and 3.5, look very carefully around the intake manifold and you will see it if its leaking! operating the engine with a coolant/oil mix can result in internal engine damage. Replacing the intake manifold gasket should correct these leaks. Because oil will mix with coolant if gasket is bad. Hope this helps you out! Good-Day!

underneath the exhause manifold side of the block. Look lihe round silver plugs.

There is a updated version of the intake manifold gasket set because they are so prone to leaking, a quick pressure test of the cooling system should determine if the intake is leaking or not do not exceed the rated pressure stamped on the radiator cap or serious damage can result

Vehicles: Any with the above symptoms

A cracked cylinder block will cause either:
(a) motor oil contamination of engine coolant
(b) coolant contamination of motor oil
(c) white exhaust smoke, due to coolant seeping into one or more cylinders.
(d) more than one of the above
(e) all of the above

Oil infiltrating into coolant is easy to see - drain some coolant out through the pepcock at the bottom of the radiator, and place it into a styrofoam coffee cup. Oil droplets floating on top of the green (or orange) coolant are easily seen. Or visualize oil by looking into the top of the radiator through the radiator cap.
Coolant infiltrating into and mixing with motor oil will permanently damage the engine (seizing it up through loss of lubrication), and must be prevented.
A leak from above the front suspension is, as physicians like to put it, "nonspecific", with the most likely cause a water pump seal or hose/hose connection.
A leak from near the fire wall will usually be a heater core hose, or hose connection.
A coolant leak on the same side of the engine as the water pump is a leaking water pump or water pump seal until proven otherwise.

To rule out everythng else, here's the 1999 Honda CR-V Troubleshooting Guide for Coolant Loss/Coolant Leaking:

Priority Action Part Type Cause
1 Inspect Water Pump - Worn, Cracked or Leaking Water Pump, or Water Pump gasket.
2 Inspect Head Gasket - Leaking Head Gasket.
3 Inspect Radiator - Leaking Radiator Hose(s).
4 Inspect Radiator Cap - Worn or Damaged Radiator Cap.
5 Inspect Radiator Hose - Ruptured, Cracked or Leaking Radiator Hose.
6 Inspect Freeze Plug - Leaking Freeze Plug(s).
7 Inspect Intake Manifold Gasket - Leaking, Worn, or Damaged Intake Manifold Gasket.
8 Inspect Water Outlet - Cracked, Leaking or Damaged Water Outlet.
9 Inspect Heater Control Valve - Leaking or Faulty Heater Control Valve.
10 Inspect Radiator Drain Pepcock - Loose, Damaged, or Faulty Radiator Drain Pepcock, or Pepcock O-ring.
11 Inspect Engine (DOMESTIC ONLY) - Cracked Cylinder Block Leaking Coolant into at least one Cylinder, causing white exhaust smoke.

You can buy or possibly rent a coolant system tester which pumps air into it to help locate leaks. Very simple to use. You just remove your radiator cap and replace it with the tester and pump it up to the PSI listed on your radiator cap and watch for leaks. I would pay close attention to the water pump and intake manifold gaskets. It could be something as simple as a loose radiator hose clamp. It is common for intake manifolds to leak and they expand when hot and contract when cool so the leak is more noticable after sitting. Look on top of the engine around your intake manifold and your heater hose for coolant or a chalky like residue which can form from coolant leaking. Your water pump has what is called a weep hole on it which will be located behind the pulley close to the shaft. You may need to use a mirror to see it. If coolant is leaking out of it the water pump will need replaced.

if you dont have a hole in your radiator hose then you have a bad water pump. when they go bad fluid leaks out the front of your motor. best of luck to you.

it may be a bad head gasket if it is leaking coolant. check to find the source of the leak. or if its leaking coolant from intake manifold gasket. also check water pump and all hoses.

it could but- check passenger side front where heater core line go into manifold right behind alternator the hose line is connected by a press clip into an alloy fitting this fitting gets eaten away by anti freeze and hose angle pulls back on fitting the part is $18 at dealer and is screwed into manifold use caution if ur r going to replace at very edge of aluminum manifold---and check ur water pump bolts the 2 longer ones should have a lock sealant on them they bolt in thru a water jacket

When they changed the water pump and the leak stopped then the water pump was bad. If they changed the water pump and was still leaking then then it was not the water pump. 
Where is the fluid leaking from, if there is white smoke coming from the tail pipe then good chance is that the head gasket is gone and pull the dip stick out to see if there is antifreeze mixxing with the engine oil.
It's common that the 3.4 V6 has intake manifold gasket go bad and leak. Check all the heater hose first, and try to find out where the leak is coming from.
Good luck and keep me posted, glad to help you as much as i can.