The smell can be caused by anaerobic air pockets forming in the substrate as shellieca said. You want to disturb these pockets with the poking process to avoid them building up to large amounts. When they break lose and they are large, they essentially poison the water. The air pockets will eventually stop forming (after the plants take hold), and the smell should subside as well, but until then you just have smelly water. I found that an air stone helps the water keep from becoming "thick" during this time. The bad side effect of that though is that it does throw the smell out of the tank more, making it more noticeable in the room.