I think exhaust gasses may be leaking into my cooling system or maybe it's oil. I replaced the intake manifold gasket a little while back and soon after noticed that the coolant in my car started turning brown. I flushed it and a little while later the fresh coolant turned nasty brown again. In the reservor I noticed that there is like brown soot in the bottom that wasn't there before. When I smell the coolant in the reservor it smells like exhaust gas.
I never had a problem like this until I replaced the intake manifold gasket. I had to have new threads installed on the thermostat housing that's why the intake had to be removed.

 

I cant see how exhaust gases can leak from the intake manifold into the cooling system very easily. Sounds very unlikely to me. Sounds more like rust in the cooling system. Do you have antifreeze in there?

The best way to check requires a tool you wont have, its a dye tester. Any decent shop should have one, shouldnt cost too much to have it checked out. If its a really bad leak, when you fire it up when its cold (make sure theres no pressure in the cooling system first) and let it run for about a minute (increasing the RPMs will help make the problem show up) and carefully take the cap off, there will be pressure in the cooling system already. Checking the top radiator hose by squeezing it is a good idea to find out how much pressure is in there, hot coolant spraying all over the place is no fun... thats why you should do it when the car is cold.

 

I doubt it's exhaust gas. If it was, like with a cracked head or something similar, the coolant would be steaming hot in a very short time. I think I'd go along with the rust idea. Back flush the system and try again.

 

If it happens to be oil which is possible, it will turn into kinda a brown/tan/grey mud

Sorry the color isn't so descriptive, but i've seen some weird things