Off tastes can be produced by the yeast used. If there is a yeasty (or bready) taste I would assume that the yeast is in suspension and you are tasting it. This may be due to a yeast with low flocculation (it doesn't clump together well). In beer, low flocculating yeast just needs to be given time to settle, but in root beer we bottle immediately and chill after only a few days.
Different yeasts also produce different biproducts. Even the same yeast can act differently depending on what type of sugar you are feeding it. Do your "biproducts" always smell the same? Hehe.
Skunky smells can occur just like in beer. This is usually due to a reaction between sunlight and hops. If you have no hops, this is unlikely to occur I think. This is why beer is sold in brown bottles.
Some effects in beer are caused by not aerating the wort enough. The yeast doesn't get enough oxygen. However, for our purposes, the yeast should get more than enough to produce the correct carbonation. If you aerate too much, you can get over carbonation.
In soft drinks, consider your water, the type of sweetener you use, and whether you have sterilized the bottles and all equipment properly.
If you don't sterilize well you may get wild yeast strains growing in the bottles, and possibly bacteria. Both can make the soda taste funny.
Here are some off-flavors in beer:
http://www.brewmaxer.com/articles/Common_Off_Flavors_In_Beer.html
Parsa